5-35947429-C-G

Variant names:

• chr5-35947429-C-G
• rs13172042

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 0.768 in 152,096 control chromosomes in the GnomAD database, including 45,200 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 0.77 (45200 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 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: 0.768 AC: 116736 AN: 151978 Hom.: 45145 Cov.: 31

Gnomad AFR AF: 0.855

Gnomad AMI AF: 0.614

Gnomad AMR AF: 0.782

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.769

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.729

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.768 AC: 116853 AN: 152096 Hom.: 45200 Cov.: 31 AF XY: 0.767 AC XY: 57003 AN XY: 74326

Gnomad4 AFR AF: 0.855

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.770

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.775

Alfa AF: 0.651 Hom.: 1809

Bravo AF: 0.782

Asia WGS AF: 0.808 AC: 2808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.38
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13172042; hg19: chr5-35947531;