rs10490071

chr2-60441755-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 0.192 in 152,110 control chromosomes in the GnomAD database, including 3,322 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 0.19 (3322 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

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 (NFE) allele frequency at 95% confidence interval = 0.259 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: 0.192 AC: 29213 AN: 151992 Hom.: 3325 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.00404

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.192 AC: 29203 AN: 152110 Hom.: 3322 Cov.: 32 AF XY: 0.188 AC XY: 13976 AN XY: 74336

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.00405

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.262

Gnomad4 OTH AF: 0.159

Alfa AF: 0.229 Hom.: 3028

Bravo AF: 0.177

Asia WGS AF: 0.0560 AC: 193 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	6.6
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10490071; hg19: chr2-60668890;