chr6-31376517-T-A

Variant names:

• chr6-31376517-T-A
• rs3997982
• ENST00000755446.1:n.327-5463T>A

Variant summary

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

The ENST00000755446.1(ENSG00000298426):​n.327-5463T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,102 control chromosomes in the GnomAD database, including 54,701 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 0.85 (54701 hom., cov: 32)
• Consequence: ENSG00000298426 ENST00000755446.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747
• Publications: 17 publications found

Genes affected

ENSG00000298426 (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 (SAS) allele frequency at 95% confidence interval = 0.911 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000755446.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298426	ENST00000755446.1		n.327-5463T>A		intron	N/A
	ENSG00000298474	ENST00000755731.1		n.304-1026A>T		intron	N/A
	ENSG00000285647	ENST00000649421.2		n.*249T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128783 AN: 151984 Hom.: 54652 Cov.: 32

Gnomad AFR AF: 0.833

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.891

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.931

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.829

Gnomad OTH AF: 0.877

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

GnomAD4 genome AF: 0.847 AC: 128888 AN: 152102 Hom.: 54701 Cov.: 32 AF XY: 0.851 AC XY: 63265 AN XY: 74340

African (AFR) AF: 0.833 AC: 34571 AN: 41490

American (AMR) AF: 0.891 AC: 13636 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.925 AC: 3208 AN: 3468

East Asian (EAS) AF: 0.931 AC: 4822 AN: 5178

South Asian (SAS) AF: 0.934 AC: 4509 AN: 4828

European-Finnish (FIN) AF: 0.837 AC: 8844 AN: 10568

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.829 AC: 56332 AN: 67956

Other (OTH) AF: 0.879 AC: 1853 AN: 2108

Alfa AF: 0.826 Hom.: 6144

Bravo AF: 0.848

Asia WGS AF: 0.920 AC: 3201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	7.8
DANN	Benign	0.71
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs3997982; hg19: chr6-31344294;