ENST00000763344.1:n.305-8496T>C

Variant names:

• chr6-137885646-A-G
• rs642627
• ENST00000763344.1:n.305-8496T>C

Variant summary

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

The ENST00000763344.1(ENSG00000287393):​n.305-8496T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 151,836 control chromosomes in the GnomAD database, including 37,707 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 0.70 (37707 hom., cov: 30)
• Consequence: ENSG00000287393 ENST00000763344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803
• Publications: 6 publications found

Genes affected

ENSG00000287393 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.886 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763344.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287393	ENST00000763344.1		n.305-8496T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106577 AN: 151718 Hom.: 37676 Cov.: 30

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.908

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.725

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

GnomAD4 genome AF: 0.702 AC: 106657 AN: 151836 Hom.: 37707 Cov.: 30 AF XY: 0.702 AC XY: 52042 AN XY: 74164

African (AFR) AF: 0.640 AC: 26481 AN: 41400

American (AMR) AF: 0.721 AC: 11004 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2346 AN: 3466

East Asian (EAS) AF: 0.908 AC: 4691 AN: 5168

South Asian (SAS) AF: 0.752 AC: 3617 AN: 4808

European-Finnish (FIN) AF: 0.674 AC: 7066 AN: 10488

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49085 AN: 67920

Other (OTH) AF: 0.727 AC: 1535 AN: 2112

Alfa AF: 0.706 Hom.: 4720

Bravo AF: 0.703

Asia WGS AF: 0.808 AC: 2807 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.31
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs642627; hg19: chr6-138206783; COSMIC: COSV52797711;