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. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

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

African (AFR) AF: 0.0325 AC: 1348 AN: 41520

American (AMR) AF: 0.0731 AC: 1115 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0292 AC: 141 AN: 4826

European-Finnish (FIN) AF: 0.213 AC: 2244 AN: 10546

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.192 AC: 13031 AN: 67950

Other (OTH) AF: 0.0938 AC: 198 AN: 2112

Alfa AF: 0.160 Hom.: 3538

Bravo AF: 0.108

Asia WGS AF: 0.0180 AC: 62 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.2
DANN	Benign	0.58
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs10494996; hg19: chr1-215419671;