rs10021692

chr4-187159831-G-A

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 0.122 in 152,110 control chromosomes in the GnomAD database, including 1,209 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 0.12 (1209 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18621 AN: 151992 Hom.: 1206 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.0746

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.122 AC: 18633 AN: 152110 Hom.: 1209 Cov.: 32 AF XY: 0.126 AC XY: 9371 AN XY: 74350

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.156

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.0742

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.103

Alfa AF: 0.109 Hom.: 1198

Bravo AF: 0.119

Asia WGS AF: 0.0860 AC: 299 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.4
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10021692; hg19: chr4-188080985;