rs4773082

Variant names:

• chr13-109751112-T-C
• rs4773082

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 0.399 in 151,810 control chromosomes in the GnomAD database, including 13,039 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 0.40 (13039 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.465 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: 0.399 AC: 60585 AN: 151694 Hom.: 13044 Cov.: 31

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.399 AC: 60584 AN: 151810 Hom.: 13039 Cov.: 31 AF XY: 0.402 AC XY: 29840 AN XY: 74160

African (AFR) AF: 0.240 AC: 9931 AN: 41396

American (AMR) AF: 0.395 AC: 6034 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1888 AN: 3468

East Asian (EAS) AF: 0.280 AC: 1439 AN: 5144

South Asian (SAS) AF: 0.466 AC: 2232 AN: 4794

European-Finnish (FIN) AF: 0.541 AC: 5702 AN: 10538

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31840 AN: 67894

Other (OTH) AF: 0.441 AC: 932 AN: 2114

Alfa AF: 0.395 Hom.: 1806

Bravo AF: 0.379

Asia WGS AF: 0.383 AC: 1329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.8
DANN	Benign	0.53
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4773082; hg19: chr13-110403459;