11-107610792-C-T

Variant names:

• chr11-107610792-C-T
• rs10431058
• NM_018712.4:c.-85-7313C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018712.4(ELMOD1):​c.-85-7313C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,544 control chromosomes in the GnomAD database, including 12,343 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (12343 hom., cov: 30)
• Consequence: ELMOD1 NM_018712.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 13 publications found

Genes affected

ELMOD1 (HGNC:25334): (ELMO domain containing 1) Enables GTPase activator activity. Predicted to be involved in positive regulation of GTPase activity. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018712.4. 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
	ELMOD1	NM_018712.4	MANE Select	c.-85-7313C>T		intron	N/A	NP_061182.3
	ELMOD1	NM_001308018.2		c.-239-7313C>T		intron	N/A	NP_001294947.1
	ELMOD1	NM_001130037.2		c.-85-7313C>T		intron	N/A	NP_001123509.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELMOD1	ENST00000265840.12	TSL:1 MANE Select	c.-85-7313C>T		intron	N/A	ENSP00000265840.7
	ELMOD1	ENST00000531234.5	TSL:2	c.-239-7313C>T		intron	N/A	ENSP00000433232.1
	ELMOD1	ENST00000443271.2	TSL:2	c.-85-7313C>T		intron	N/A	ENSP00000412257.2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 57995 AN: 151430 Hom.: 12338 Cov.: 30

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.398

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.401

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58020 AN: 151544 Hom.: 12343 Cov.: 30 AF XY: 0.391 AC XY: 28964 AN XY: 73998

African (AFR) AF: 0.225 AC: 9297 AN: 41372

American (AMR) AF: 0.512 AC: 7792 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.416 AC: 1441 AN: 3466

East Asian (EAS) AF: 0.714 AC: 3693 AN: 5172

South Asian (SAS) AF: 0.398 AC: 1913 AN: 4804

European-Finnish (FIN) AF: 0.499 AC: 5154 AN: 10330

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.403 AC: 27378 AN: 67872

Other (OTH) AF: 0.402 AC: 844 AN: 2100

Alfa AF: 0.398 Hom.: 30922

Bravo AF: 0.378

Asia WGS AF: 0.540 AC: 1877 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.38
PhyloP100		-0.38
Mutation Taster		=100/0	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: rs10431058; hg19: chr11-107481518;