13-110930649-C-T

Variant names:

• chr13-110930649-C-T
• rs9521996

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 0.812 in 152,194 control chromosomes in the GnomAD database, including 50,435 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 0.81 (50435 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840
• 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 = 0.898 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: 0.812 AC: 123472 AN: 152076 Hom.: 50402 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.897

Gnomad AMR AF: 0.839

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.812 AC: 123562 AN: 152194 Hom.: 50435 Cov.: 32 AF XY: 0.813 AC XY: 60480 AN XY: 74404

African (AFR) AF: 0.725 AC: 30075 AN: 41490

American (AMR) AF: 0.840 AC: 12847 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3118 AN: 3472

East Asian (EAS) AF: 0.920 AC: 4757 AN: 5172

South Asian (SAS) AF: 0.811 AC: 3914 AN: 4826

European-Finnish (FIN) AF: 0.837 AC: 8879 AN: 10606

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57124 AN: 68004

Other (OTH) AF: 0.835 AC: 1767 AN: 2116

Alfa AF: 0.822 Hom.: 8229

Bravo AF: 0.809

Asia WGS AF: 0.865 AC: 3008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.4
DANN	Benign	0.46
PhyloP100		0.084

Splicing

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

Other links and lift over

dbSNP: rs9521996; hg19: chr13-111582996;