rs6591182

Variant names:

• chr11-65582285-T-G
• rs6591182
• NM_001099409.3:c.1613T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-65582285-T-G
• chr11-65582285-T-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001099409.3(EHBP1L1):​c.1613T>G​(p.Val538Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 1,527,610 control chromosomes in the GnomAD database, including 181,234 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.45 (16336 hom., cov: 33)
  • Exomes 𝑓: 0.49 (164898 hom.)
• Consequence: EHBP1L1 NM_001099409.3 missense
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.116
• Publications: 61 publications found

Genes affected

EHBP1L1 (HGNC:30682): (EH domain binding protein 1 like 1) Predicted to be involved in actin cytoskeleton organization. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=4.8787624E-5).
• BP6: Variant 11-65582285-T-G is Benign according to our data. Variant chr11-65582285-T-G is described in ClinVar as Benign. ClinVar VariationId is 1265858.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001099409.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1L1	NM_001099409.3	MANE Select	c.1613T>G	p.Val538Gly	missense	Exon 9 of 19	NP_001092879.1	Q8N3D4
	EHBP1L1	NM_001351087.2		c.819+959T>G		intron	N/A	NP_001338016.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EHBP1L1	ENST00000309295.9	TSL:1 MANE Select	c.1613T>G	p.Val538Gly	missense	Exon 9 of 19	ENSP00000312671.4	Q8N3D4
	EHBP1L1	ENST00000968317.1		c.1649T>G	p.Val550Gly	missense	Exon 10 of 20	ENSP00000638376.1
	EHBP1L1	ENST00000968331.1		c.1649T>G	p.Val550Gly	missense	Exon 10 of 18	ENSP00000638390.1

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68815 AN: 151824 Hom.: 16332 Cov.: 33

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.544

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.467

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.619

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.480

GnomAD2 exomes AF: 0.475 AC: 80724 AN: 169966 AF XY: 0.484

Gnomad AFR exome AF: 0.322

Gnomad AMR exome AF: 0.351

Gnomad ASJ exome AF: 0.453

Gnomad EAS exome AF: 0.464

Gnomad FIN exome AF: 0.608

Gnomad NFE exome AF: 0.497

Gnomad OTH exome AF: 0.494

GnomAD4 exome AF: 0.487 AC: 670315 AN: 1375666 Hom.: 164898 Cov.: 86 AF XY: 0.489 AC XY: 331097 AN XY: 676658

African (AFR) AF: 0.322 AC: 9809 AN: 30444

American (AMR) AF: 0.357 AC: 10469 AN: 29326

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 9144 AN: 20152

East Asian (EAS) AF: 0.441 AC: 17258 AN: 39126

South Asian (SAS) AF: 0.529 AC: 37889 AN: 71574

European-Finnish (FIN) AF: 0.600 AC: 29211 AN: 48660

Middle Eastern (MID) AF: 0.460 AC: 2437 AN: 5296

European-Non Finnish (NFE) AF: 0.491 AC: 527743 AN: 1074556

Other (OTH) AF: 0.466 AC: 26355 AN: 56532

GnomAD4 genome AF: 0.453 AC: 68848 AN: 151944 Hom.: 16336 Cov.: 33 AF XY: 0.459 AC XY: 34079 AN XY: 74288

African (AFR) AF: 0.328 AC: 13583 AN: 41380

American (AMR) AF: 0.402 AC: 6138 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.453 AC: 1571 AN: 3468

East Asian (EAS) AF: 0.466 AC: 2401 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2489 AN: 4826

European-Finnish (FIN) AF: 0.619 AC: 6556 AN: 10594

Middle Eastern (MID) AF: 0.435 AC: 128 AN: 294

European-Non Finnish (NFE) AF: 0.507 AC: 34464 AN: 67928

Other (OTH) AF: 0.484 AC: 1022 AN: 2110

Alfa AF: 0.478 Hom.: 69677

Bravo AF: 0.426

TwinsUK AF: 0.487 AC: 1805

ALSPAC AF: 0.496 AC: 1910

ESP6500AA AF: 0.315 AC: 1180

ESP6500EA AF: 0.474 AC: 3862

ExAC AF: 0.458 AC: 53907

Asia WGS AF: 0.469 AC: 1631 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.091
BayesDel_addAF	Benign	-0.53	T
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Uncertain	1.0
DEOGEN2	Benign	0.072	T
Eigen	Uncertain	0.21
Eigen_PC	Benign	0.22
FATHMM_MKL	Uncertain	0.80	D
LIST_S2	Benign	0.27	T
MetaRNN	Benign	0.000049	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	1.1	L
PhyloP100		-0.12
PrimateAI	Benign	0.34	T
PROVEAN	Uncertain	-3.0	D
REVEL	Benign	0.25
Sift	Benign	0.095	T
Sift4G	Benign	0.21	T
Polyphen		0.96	P
Vest4		0.078
MPC		0.051
ClinPred		0.025	T
GERP RS		3.8
PromoterAI		-0.057	Neutral
Varity_R		0.28
gMVP		0.35
Mutation Taster		=91/9	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6591182; hg19: chr11-65349756; COSMIC: COSV58573279; COSMIC: COSV58573279;