rs13082711

Variant names:

• chr3-27496418-T-C
• rs13082711
• ENST00000826604.1:n.683+2970T>C

Variant summary

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

The ENST00000826604.1(ENSG00000307499):​n.683+2970T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,048 control chromosomes in the GnomAD database, including 2,418 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 0.16 (2418 hom., cov: 31)
• Consequence: ENSG00000307499 ENST00000826604.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 64 publications found

Genes affected

ENSG00000307499 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.226 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
ENSG00000307499	ENST00000826604.1	n.683+2970T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25013 AN: 151930 Hom.: 2419 Cov.: 31

Gnomad AFR AF: 0.0662

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0462

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.165 AC: 25020 AN: 152048 Hom.: 2418 Cov.: 31 AF XY: 0.161 AC XY: 11962 AN XY: 74308

African (AFR) AF: 0.0661 AC: 2743 AN: 41524

American (AMR) AF: 0.167 AC: 2551 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.0463 AC: 239 AN: 5166

South Asian (SAS) AF: 0.166 AC: 798 AN: 4814

European-Finnish (FIN) AF: 0.180 AC: 1896 AN: 10562

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15591 AN: 67964

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.205 Hom.: 10385

Bravo AF: 0.159

Asia WGS AF: 0.145 AC: 502 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.0
DANN	Benign	0.80
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs13082711; hg19: chr3-27537909;