4-177097994-G-T

Variant names:

• chr4-177097994-G-T
• rs6846031
• ENST00000656694.1:n.346+12626C>A

Variant summary

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

The ENST00000656694.1(ENSG00000287544):​n.346+12626C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,742 control chromosomes in the GnomAD database, including 15,513 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 0.45 (15513 hom., cov: 30)
• Consequence: ENSG00000287544 ENST00000656694.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 8 publications found

Genes affected

ENSG00000287544 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000656694.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287544	ENST00000656694.1		n.346+12626C>A		intron	N/A
	ENSG00000287544	ENST00000662794.1		n.419+12626C>A		intron	N/A
	ENSG00000287544	ENST00000667713.1		n.594+12626C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68421 AN: 151626 Hom.: 15503 Cov.: 30

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.535

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.507

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.451 AC: 68456 AN: 151742 Hom.: 15513 Cov.: 30 AF XY: 0.444 AC XY: 32883 AN XY: 74138

African (AFR) AF: 0.425 AC: 17557 AN: 41354

American (AMR) AF: 0.407 AC: 6206 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.507 AC: 1752 AN: 3458

East Asian (EAS) AF: 0.439 AC: 2256 AN: 5136

South Asian (SAS) AF: 0.397 AC: 1907 AN: 4804

European-Finnish (FIN) AF: 0.372 AC: 3908 AN: 10506

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.490 AC: 33257 AN: 67914

Other (OTH) AF: 0.462 AC: 973 AN: 2104

Alfa AF: 0.474 Hom.: 45692

Bravo AF: 0.449

Asia WGS AF: 0.414 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.8
DANN	Benign	0.54
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs6846031; hg19: chr4-178019148;