chr6-31461190-G-A

Variant names:

• chr6-31461190-G-A
• rs2596472
• ENST00000673857.1:n.63-1933G>A

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-1933G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 151,872 control chromosomes in the GnomAD database, including 44,147 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 0.76 (44147 hom., cov: 32)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.263
• Publications: 28 publications found

Genes affected

ENSG00000288587 (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 = 0.898 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
ENSG00000288587	ENST00000673857.1	n.63-1933G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115151 AN: 151754 Hom.: 44095 Cov.: 32

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.776

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.819

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.759 AC: 115261 AN: 151872 Hom.: 44147 Cov.: 32 AF XY: 0.756 AC XY: 56138 AN XY: 74236

African (AFR) AF: 0.792 AC: 32731 AN: 41304

American (AMR) AF: 0.736 AC: 11192 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.776 AC: 2693 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4756 AN: 5170

South Asian (SAS) AF: 0.819 AC: 3954 AN: 4828

European-Finnish (FIN) AF: 0.658 AC: 6952 AN: 10564

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.741 AC: 50381 AN: 67998

Other (OTH) AF: 0.776 AC: 1641 AN: 2114

Alfa AF: 0.759 Hom.: 76920

Bravo AF: 0.766

Asia WGS AF: 0.863 AC: 3002 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.49
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2596472; hg19: chr6-31428967;