chr13-22982476-C-T

Variant names:

• chr13-22982476-C-T
• rs943386

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 0.575 in 151,990 control chromosomes in the GnomAD database, including 26,475 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 0.58 (26475 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.673 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: 0.575 AC: 87384 AN: 151870 Hom.: 26459 Cov.: 33

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.679

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.575 AC: 87441 AN: 151990 Hom.: 26475 Cov.: 33 AF XY: 0.571 AC XY: 42398 AN XY: 74252

African (AFR) AF: 0.457 AC: 18917 AN: 41432

American (AMR) AF: 0.488 AC: 7461 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.714 AC: 2473 AN: 3466

East Asian (EAS) AF: 0.217 AC: 1118 AN: 5160

South Asian (SAS) AF: 0.459 AC: 2214 AN: 4822

European-Finnish (FIN) AF: 0.681 AC: 7179 AN: 10540

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.679 AC: 46122 AN: 67964

Other (OTH) AF: 0.602 AC: 1272 AN: 2112

Alfa AF: 0.641 Hom.: 17588

Bravo AF: 0.554

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.28
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs943386; hg19: chr13-23556615;