rs10494997

Variant names:

• chr1-215286704-G-A
• rs10494997

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 0.174 in 151,644 control chromosomes in the GnomAD database, including 2,392 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 0.17 (2392 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.19 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: 0.174 AC: 26412 AN: 151526 Hom.: 2392 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.0733

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.303

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.174 AC: 26417 AN: 151644 Hom.: 2392 Cov.: 32 AF XY: 0.168 AC XY: 12451 AN XY: 74122

African (AFR) AF: 0.174 AC: 7214 AN: 41384

American (AMR) AF: 0.168 AC: 2553 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 679 AN: 3466

East Asian (EAS) AF: 0.0734 AC: 377 AN: 5134

South Asian (SAS) AF: 0.128 AC: 615 AN: 4804

European-Finnish (FIN) AF: 0.111 AC: 1170 AN: 10570

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.193 AC: 13062 AN: 67796

Other (OTH) AF: 0.206 AC: 434 AN: 2102

Alfa AF: 0.190 Hom.: 12165

Bravo AF: 0.181

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.68
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs10494997; hg19: chr1-215460047;