5-35947429-C-G

Variant names:

• chr5-35947429-C-G
• rs13172042

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 0.768 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.855 AC: 35501 AN: 41514

American (AMR) AF: 0.782 AC: 11959 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3470

East Asian (EAS) AF: 0.913 AC: 4723 AN: 5172

South Asian (SAS) AF: 0.770 AC: 3697 AN: 4804

European-Finnish (FIN) AF: 0.656 AC: 6914 AN: 10542

Middle Eastern (MID) AF: 0.733 AC: 214 AN: 292

European-Non Finnish (NFE) AF: 0.723 AC: 49132 AN: 67988

Other (OTH) AF: 0.775 AC: 1634 AN: 2108

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
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs13172042; hg19: chr5-35947531;