rs4390682

Variant names:

• chr18-51026083-G-A
• rs4390682
• ENST00000590722.2:n.158-20837G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-51026083-G-A
• chr18-51026083-G-C
• chr18-51026083-G-T

Variant summary

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

The ENST00000590722.2(ENSG00000267699):​n.158-20837G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.422 in 151,960 control chromosomes in the GnomAD database, including 13,658 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 0.42 (13658 hom., cov: 32)
• Consequence: ENSG00000267699 ENST00000590722.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.259
• Publications: 6 publications found

Genes affected

ENSG00000267699 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985152	XR_007066370.1	n.177+3835C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000267699	ENST00000590722.2	n.158-20837G>A		intron_variant	Intron 2 of 8	2		ENSP00000465737.1

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64003 AN: 151842 Hom.: 13641 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.422 AC: 64081 AN: 151960 Hom.: 13658 Cov.: 32 AF XY: 0.419 AC XY: 31117 AN XY: 74278

African (AFR) AF: 0.493 AC: 20432 AN: 41418

American (AMR) AF: 0.402 AC: 6144 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1423 AN: 3466

East Asian (EAS) AF: 0.453 AC: 2335 AN: 5158

South Asian (SAS) AF: 0.259 AC: 1246 AN: 4814

European-Finnish (FIN) AF: 0.407 AC: 4296 AN: 10564

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.392 AC: 26604 AN: 67948

Other (OTH) AF: 0.436 AC: 921 AN: 2110

Alfa AF: 0.386 Hom.: 5310

Bravo AF: 0.432

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.57
PhyloP100		-0.26
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: rs4390682; hg19: chr18-48552453;