13-83874717-T-C

Variant names:

• chr13-83874717-T-C
• rs9593835

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 0.304 in 151,888 control chromosomes in the GnomAD database, including 7,363 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 0.30 (7363 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.969
• Publications: 9 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 (EAS) allele frequency at 95% confidence interval = 0.38 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: 0.304 AC: 46126 AN: 151770 Hom.: 7347 Cov.: 33

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.304 AC: 46173 AN: 151888 Hom.: 7363 Cov.: 33 AF XY: 0.303 AC XY: 22478 AN XY: 74224

African (AFR) AF: 0.368 AC: 15253 AN: 41462

American (AMR) AF: 0.328 AC: 5004 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3464

East Asian (EAS) AF: 0.394 AC: 2036 AN: 5166

South Asian (SAS) AF: 0.393 AC: 1896 AN: 4828

European-Finnish (FIN) AF: 0.176 AC: 1862 AN: 10596

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.264 AC: 17916 AN: 67782

Other (OTH) AF: 0.318 AC: 672 AN: 2112

Alfa AF: 0.283 Hom.: 23229

Bravo AF: 0.315

Asia WGS AF: 0.381 AC: 1320 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.27
DANN	Benign	0.47
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs9593835; hg19: chr13-84448852;