rs13173919

Variant names:

• chr5-7919099-T-C
• rs13173919

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 0.141 in 150,666 control chromosomes in the GnomAD database, including 2,593 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 0.14 (2593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.196
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.141 AC: 21256 AN: 150550 Hom.: 2593 Cov.: 32

Gnomad AFR AF: 0.0379

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.00144

Gnomad SAS AF: 0.0897

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.141 AC: 21260 AN: 150666 Hom.: 2593 Cov.: 32 AF XY: 0.139 AC XY: 10230 AN XY: 73528

African (AFR) AF: 0.0378 AC: 1566 AN: 41424

American (AMR) AF: 0.112 AC: 1662 AN: 14898

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3468

East Asian (EAS) AF: 0.00144 AC: 7 AN: 4858

South Asian (SAS) AF: 0.0903 AC: 430 AN: 4760

European-Finnish (FIN) AF: 0.208 AC: 2151 AN: 10342

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.211 AC: 14265 AN: 67628

Other (OTH) AF: 0.116 AC: 242 AN: 2094

Alfa AF: 0.186 Hom.: 4657

Bravo AF: 0.129

Asia WGS AF: 0.0440 AC: 150 AN: 3404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.0
DANN	Benign	0.60
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13173919; hg19: chr5-7919212;