rs193741

Variant names:

• chr5-25692864-G-A
• rs193741

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 0.815 in 152,086 control chromosomes in the GnomAD database, including 50,680 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 0.82 (50680 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.834 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: 0.815 AC: 123924 AN: 151970 Hom.: 50646 Cov.: 32

Gnomad AFR AF: 0.811

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.849

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.840

Gnomad OTH AF: 0.803

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

GnomAD4 genome AF: 0.815 AC: 124010 AN: 152086 Hom.: 50680 Cov.: 32 AF XY: 0.814 AC XY: 60479 AN XY: 74330

African (AFR) AF: 0.811 AC: 33638 AN: 41484

American (AMR) AF: 0.775 AC: 11834 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2787 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3161 AN: 5144

South Asian (SAS) AF: 0.784 AC: 3776 AN: 4814

European-Finnish (FIN) AF: 0.849 AC: 8989 AN: 10588

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.840 AC: 57099 AN: 68002

Other (OTH) AF: 0.801 AC: 1691 AN: 2112

Alfa AF: 0.829 Hom.: 95920

Bravo AF: 0.810

Asia WGS AF: 0.709 AC: 2461 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs193741; hg19: chr5-25692973;