rs13173919

chr5-7919099-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0378

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.00144

Gnomad4 SAS AF: 0.0903

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.116

Alfa AF: 0.192 Hom.: 3822

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13173919; hg19: chr5-7919212;