chr6-31424341-A-G

Variant names:

• chr6-31424341-A-G
• rs9501109
• ENST00000673857.1:n.62+23578A>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+23578A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,424 control chromosomes in the GnomAD database, including 7,394 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 0.29 (7394 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.155
• Publications: 16 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 = 0.403 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+23578A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44491 AN: 151306 Hom.: 7390 Cov.: 31

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.294 AC: 44535 AN: 151424 Hom.: 7394 Cov.: 31 AF XY: 0.297 AC XY: 21994 AN XY: 74002

African (AFR) AF: 0.408 AC: 16773 AN: 41106

American (AMR) AF: 0.369 AC: 5577 AN: 15112

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1533 AN: 3470

East Asian (EAS) AF: 0.183 AC: 940 AN: 5142

South Asian (SAS) AF: 0.267 AC: 1279 AN: 4798

European-Finnish (FIN) AF: 0.268 AC: 2833 AN: 10552

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.213 AC: 14495 AN: 67946

Other (OTH) AF: 0.314 AC: 659 AN: 2096

Alfa AF: 0.248 Hom.: 11623

Bravo AF: 0.307

Asia WGS AF: 0.266 AC: 924 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	3.7
DANN	Benign	0.37
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs9501109; hg19: chr6-31392118;