13-82322644-T-C

Variant names:

• chr13-82322644-T-C
• rs7984202

Variant summary

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

The variant allele was found at a frequency of 0.667 in 152,038 control chromosomes in the GnomAD database, including 34,541 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 0.67 (34541 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101232 AN: 151920 Hom.: 34486 Cov.: 32

Gnomad AFR AF: 0.779

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.587

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.594

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.667 AC: 101350 AN: 152038 Hom.: 34541 Cov.: 32 AF XY: 0.671 AC XY: 49885 AN XY: 74296

African (AFR) AF: 0.779 AC: 32324 AN: 41492

American (AMR) AF: 0.614 AC: 9367 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2205 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4887 AN: 5162

South Asian (SAS) AF: 0.798 AC: 3857 AN: 4832

European-Finnish (FIN) AF: 0.587 AC: 6203 AN: 10560

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.594 AC: 40392 AN: 67948

Other (OTH) AF: 0.676 AC: 1427 AN: 2112

Alfa AF: 0.617 Hom.: 35680

Bravo AF: 0.671

Asia WGS AF: 0.875 AC: 3036 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.73
DANN	Benign	0.33
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7984202; hg19: chr13-82896779;