ENST00000782490.1:n.217+1872G>A

Variant names:

• chr6-31618317-C-T
• rs2736177
• ENST00000782490.1:n.217+1872G>A

Variant summary

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

The ENST00000782490.1(ENSG00000289375):​n.217+1872G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,046 control chromosomes in the GnomAD database, including 63,705 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 0.91 (63705 hom., cov: 29)
• Consequence: ENSG00000289375 ENST00000782490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 32 publications found

Genes affected

ENSG00000289375 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782490.1. 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
	ENSG00000289375	ENST00000782490.1		n.217+1872G>A		intron	N/A
	ENSG00000289375	ENST00000782491.1		n.205-1819G>A		intron	N/A
	ENSG00000289375	ENST00000782492.1		n.152+1872G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138837 AN: 151928 Hom.: 63642 Cov.: 29

Gnomad AFR AF: 0.975

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.995

Gnomad SAS AF: 0.974

Gnomad FIN AF: 0.875

Gnomad MID AF: 0.965

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.937

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

GnomAD4 genome AF: 0.914 AC: 138958 AN: 152046 Hom.: 63705 Cov.: 29 AF XY: 0.916 AC XY: 68031 AN XY: 74308

African (AFR) AF: 0.975 AC: 40474 AN: 41502

American (AMR) AF: 0.937 AC: 14291 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3356 AN: 3472

East Asian (EAS) AF: 0.995 AC: 5150 AN: 5174

South Asian (SAS) AF: 0.974 AC: 4697 AN: 4822

European-Finnish (FIN) AF: 0.875 AC: 9226 AN: 10542

Middle Eastern (MID) AF: 0.963 AC: 283 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58658 AN: 67976

Other (OTH) AF: 0.938 AC: 1978 AN: 2108

Alfa AF: 0.888 Hom.: 153754

Bravo AF: 0.921

Asia WGS AF: 0.980 AC: 3408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	12
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2736177; hg19: chr6-31586094;