6-31426923-A-G

Variant names:

• chr6-31426923-A-G
• rs2516472
• ENST00000673857.1:n.62+26160A>G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.62+26160A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 151,804 control chromosomes in the GnomAD database, including 1,309 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 0.11 (1309 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.957
• Publications: 14 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.19 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.62+26160A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16126 AN: 151686 Hom.: 1305 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.0830

Gnomad EAS AF: 0.0100

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.112

Gnomad NFE AF: 0.0746

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.106 AC: 16146 AN: 151804 Hom.: 1309 Cov.: 31 AF XY: 0.103 AC XY: 7658 AN XY: 74232

African (AFR) AF: 0.193 AC: 7970 AN: 41264

American (AMR) AF: 0.124 AC: 1881 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.0830 AC: 288 AN: 3470

East Asian (EAS) AF: 0.0102 AC: 53 AN: 5174

South Asian (SAS) AF: 0.0859 AC: 414 AN: 4818

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10612

Middle Eastern (MID) AF: 0.107 AC: 31 AN: 290

European-Non Finnish (NFE) AF: 0.0745 AC: 5069 AN: 67996

Other (OTH) AF: 0.135 AC: 284 AN: 2108

Alfa AF: 0.0828 Hom.: 2084

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.3
DANN	Benign	0.40
PhyloP100		0.96
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2516472; hg19: chr6-31394700;