13-109919863-C-T

Variant names:

• chr13-109919863-C-T
• rs7323507

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 0.632 in 151,976 control chromosomes in the GnomAD database, including 30,504 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 0.63 (30504 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.67 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: 0.632 AC: 95992 AN: 151858 Hom.: 30487 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.626

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.632 AC: 96048 AN: 151976 Hom.: 30504 Cov.: 31 AF XY: 0.625 AC XY: 46476 AN XY: 74308

African (AFR) AF: 0.584 AC: 24174 AN: 41402

American (AMR) AF: 0.616 AC: 9410 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2215 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3228 AN: 5154

South Asian (SAS) AF: 0.584 AC: 2817 AN: 4820

European-Finnish (FIN) AF: 0.574 AC: 6060 AN: 10554

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45867 AN: 67980

Other (OTH) AF: 0.640 AC: 1351 AN: 2110

Alfa AF: 0.656 Hom.: 25410

Bravo AF: 0.636

Asia WGS AF: 0.567 AC: 1973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.89
DANN	Benign	0.45
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7323507; hg19: chr13-110572210;