rs10019942

Variant names:

• chr4-100932637-T-C
• rs10019942

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 0.233 in 152,060 control chromosomes in the GnomAD database, including 5,938 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 0.23 (5938 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35337 AN: 151942 Hom.: 5890 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.233 AC: 35456 AN: 152060 Hom.: 5938 Cov.: 32 AF XY: 0.232 AC XY: 17264 AN XY: 74330

African (AFR) AF: 0.474 AC: 19663 AN: 41464

American (AMR) AF: 0.168 AC: 2568 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 509 AN: 3470

East Asian (EAS) AF: 0.107 AC: 554 AN: 5170

South Asian (SAS) AF: 0.193 AC: 928 AN: 4812

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10596

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8995 AN: 67968

Other (OTH) AF: 0.184 AC: 389 AN: 2110

Alfa AF: 0.198 Hom.: 687

Bravo AF: 0.245

Asia WGS AF: 0.216 AC: 750 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.3
DANN	Benign	0.77
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs10019942; hg19: chr4-101853794;