rs2241970

chr10-68271310-A-G

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 0.139 in 152,270 control chromosomes in the GnomAD database, including 1,965 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 0.14 (1965 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0810

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 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: 0.139 AC: 21118 AN: 152152 Hom.: 1964 Cov.: 32

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.271

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.240

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.139 AC: 21126 AN: 152270 Hom.: 1965 Cov.: 32 AF XY: 0.144 AC XY: 10725 AN XY: 74448

Gnomad4 AFR AF: 0.0314

Gnomad4 AMR AF: 0.214

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.142

Alfa AF: 0.167 Hom.: 1207

Bravo AF: 0.136

Asia WGS AF: 0.173 AC: 602 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	7.3
Dann	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2241970; hg19: chr10-70031067;