rs2524276

Variant names:

• chr6-31440488-C-A
• rs2524276
• ENST00000673857.1:n.63-22635C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-31440488-C-A
• chr6-31440488-C-G
• chr6-31440488-C-T

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-22635C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0673 in 151,824 control chromosomes in the GnomAD database, including 552 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 0.067 (552 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.577
• Publications: 30 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0885 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.63-22635C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0673 AC: 10207 AN: 151706 Hom.: 551 Cov.: 31

Gnomad AFR AF: 0.0855

Gnomad AMI AF: 0.0264

Gnomad AMR AF: 0.0927

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.00965

Gnomad SAS AF: 0.0804

Gnomad FIN AF: 0.00727

Gnomad MID AF: 0.0414

Gnomad NFE AF: 0.0644

Gnomad OTH AF: 0.0907

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

GnomAD4 genome AF: 0.0673 AC: 10218 AN: 151824 Hom.: 552 Cov.: 31 AF XY: 0.0646 AC XY: 4791 AN XY: 74212

African (AFR) AF: 0.0855 AC: 3531 AN: 41288

American (AMR) AF: 0.0925 AC: 1406 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.0467 AC: 162 AN: 3472

East Asian (EAS) AF: 0.00986 AC: 51 AN: 5170

South Asian (SAS) AF: 0.0805 AC: 387 AN: 4810

European-Finnish (FIN) AF: 0.00727 AC: 77 AN: 10588

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0644 AC: 4379 AN: 67998

Other (OTH) AF: 0.0893 AC: 188 AN: 2106

Alfa AF: 0.0615 Hom.: 1284

Bravo AF: 0.0763

Asia WGS AF: 0.0470 AC: 161 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.8
DANN	Benign	0.68
PhyloP100		0.58
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: rs2524276; hg19: chr6-31408265;