rs10490071

Variant names:

• chr2-60441755-G-A
• rs10490071

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.104 AC: 4326 AN: 41510

American (AMR) AF: 0.147 AC: 2243 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3464

East Asian (EAS) AF: 0.00405 AC: 21 AN: 5182

South Asian (SAS) AF: 0.117 AC: 561 AN: 4812

European-Finnish (FIN) AF: 0.286 AC: 3016 AN: 10558

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17809 AN: 67976

Other (OTH) AF: 0.159 AC: 335 AN: 2112

Alfa AF: 0.228 Hom.: 3592

Bravo AF: 0.177

Asia WGS AF: 0.0560 AC: 193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.6
DANN	Benign	0.62
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10490071; hg19: chr2-60668890;