rs10490071

Variant names:

• chr2-60441755-G-A
• rs10490071

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;