3-179633577-C-T

Variant names:

• chr3-179633577-C-T
• rs6443662
• ENST00000680408.1:n.*79-6287C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000680408.1(ENSG00000288698):​n.*79-6287C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 152,100 control chromosomes in the GnomAD database, including 25,430 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 0.57 (25430 hom., cov: 32)
• Consequence: ENSG00000288698 ENST00000680408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000288698 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.751 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
ENSG00000288698	ENST00000680408.1	n.*79-6287C>T		intron_variant	Intron 4 of 25			ENSP00000506198.1
ENSG00000288698	ENST00000680407.1	n.30+7631C>T		intron_variant	Intron 1 of 1
ENSG00000288698	ENST00000680692.1	n.107+15056C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86410 AN: 151982 Hom.: 25425 Cov.: 32

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.771

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.568 AC: 86455 AN: 152100 Hom.: 25430 Cov.: 32 AF XY: 0.575 AC XY: 42725 AN XY: 74362

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.771

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.622

Gnomad4 OTH AF: 0.635

Alfa AF: 0.597 Hom.: 5671

Bravo AF: 0.562

Asia WGS AF: 0.678 AC: 2357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.52
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6443662; hg19: chr3-179351365;