rs10019942

Variant names:

• chr4-100932637-T-C
• rs10019942

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 0.233 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.233 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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.107

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.184

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10019942; hg19: chr4-101853794;