rs10494997

Positions:

• chr1-215286704-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 0.174 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;