rs10494997

Variant names:

• chr1-215286704-G-A
• rs10494997

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 0.174 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.174 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

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.196

Gnomad4 EAS AF: 0.0734

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.206

Alfa AF: 0.194 Hom.: 6066

Bravo AF: 0.181

Asia WGS AF: 0.112 AC: 390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494997; hg19: chr1-215460047;