rs10494996

Variant names:

• chr1-215246328-G-A
• rs10494996

Your query was ambiguous. Multiple possible variants found:

• chr1-215246328-G-A
• chr1-215246328-G-C
• chr1-215246328-G-T

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 0.123 in 152,040 control chromosomes in the GnomAD database, including 1,660 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 0.12 (1660 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.189 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: 0.123 AC: 18677 AN: 151922 Hom.: 1661 Cov.: 33

Gnomad AFR AF: 0.0326

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.0947

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

GnomAD4 genome AF: 0.123 AC: 18670 AN: 152040 Hom.: 1660 Cov.: 33 AF XY: 0.121 AC XY: 8979 AN XY: 74344

Gnomad4 AFR AF: 0.0325

Gnomad4 AMR AF: 0.0731

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.0292

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.0938

Alfa AF: 0.164 Hom.: 2898

Bravo AF: 0.108

Asia WGS AF: 0.0180 AC: 62 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494996; hg19: chr1-215419671;