rs2524082

Variant names:

• chr6-31273984-A-T
• rs2524082
• ENST00000755297.1:n.32+2878A>T

Variant summary

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

The ENST00000755297.1(ENSG00000298396):​n.32+2878A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 149,390 control chromosomes in the GnomAD database, including 22,219 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 0.54 (22219 hom., cov: 25)
• Consequence: ENSG00000298396 ENST00000755297.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 13 publications found

Genes affected

ENSG00000298396 (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 (SAS) allele frequency at 95% confidence interval = 0.578 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
ENSG00000298396	ENST00000755297.1	n.32+2878A>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.542 AC: 80925 AN: 149274 Hom.: 22203 Cov.: 25

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.499

Gnomad ASJ AF: 0.570

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.542 AC: 80978 AN: 149390 Hom.: 22219 Cov.: 25 AF XY: 0.542 AC XY: 39366 AN XY: 72684

African (AFR) AF: 0.524 AC: 21191 AN: 40444

American (AMR) AF: 0.499 AC: 7410 AN: 14858

Ashkenazi Jewish (ASJ) AF: 0.570 AC: 1972 AN: 3458

East Asian (EAS) AF: 0.418 AC: 2125 AN: 5086

South Asian (SAS) AF: 0.596 AC: 2832 AN: 4748

European-Finnish (FIN) AF: 0.524 AC: 5205 AN: 9930

Middle Eastern (MID) AF: 0.659 AC: 191 AN: 290

European-Non Finnish (NFE) AF: 0.570 AC: 38496 AN: 67590

Other (OTH) AF: 0.520 AC: 1079 AN: 2076

Alfa AF: 0.559 Hom.: 2997

Bravo AF: 0.543

Asia WGS AF: 0.521 AC: 1808 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.0
DANN	Benign	0.68
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2524082; hg19: chr6-31241761;