rs4738150

Variant names:

• chr8-71695672-G-A
• rs4738150
• ENST00000519840.2:n.404-6543G>A

Variant summary

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

The ENST00000519840.2(ENSG00000254277):​n.404-6543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,966 control chromosomes in the GnomAD database, including 21,446 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 0.50 (21446 hom., cov: 32)
• Consequence: ENSG00000254277 ENST00000519840.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.448
• Publications: 4 publications found

Genes affected

ENSG00000254277 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254277	ENST00000519840.2	n.404-6543G>A		intron_variant	Intron 1 of 1	2
ENSG00000254277	ENST00000521131.2	n.247-269G>A		intron_variant	Intron 1 of 2	3
ENSG00000254277	ENST00000691315.2	n.254+20137G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75772 AN: 151848 Hom.: 21437 Cov.: 32

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.685

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.389

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.499 AC: 75805 AN: 151966 Hom.: 21446 Cov.: 32 AF XY: 0.501 AC XY: 37209 AN XY: 74272

African (AFR) AF: 0.214 AC: 8874 AN: 41464

American (AMR) AF: 0.641 AC: 9768 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1834 AN: 3466

East Asian (EAS) AF: 0.592 AC: 3053 AN: 5158

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4818

European-Finnish (FIN) AF: 0.652 AC: 6896 AN: 10574

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41698 AN: 67940

Other (OTH) AF: 0.500 AC: 1053 AN: 2108

Alfa AF: 0.578 Hom.: 17664

Bravo AF: 0.492

Asia WGS AF: 0.483 AC: 1679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.8
DANN	Benign	0.64
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs4738150; hg19: chr8-72607907;