rs1642739

Positions:

• chr3-10153801-A-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 0.889 in 151,962 control chromosomes in the GnomAD database, including 60,217 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 0.89 (60217 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.892

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 (AFR) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.889 AC: 135049 AN: 151844 Hom.: 60185 Cov.: 30

Gnomad AFR AF: 0.936

Gnomad AMI AF: 0.880

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.925

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.902

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.889 AC: 135130 AN: 151962 Hom.: 60217 Cov.: 30 AF XY: 0.891 AC XY: 66155 AN XY: 74280

Gnomad4 AFR AF: 0.935

Gnomad4 AMR AF: 0.864

Gnomad4 ASJ AF: 0.925

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.902

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.872

Alfa AF: 0.871 Hom.: 80487

Bravo AF: 0.890

Asia WGS AF: 0.830 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1642739; hg19: chr3-10195485;