rs10908703

Variant names:

• chr1-159282212-G-A
• rs10908703

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 0.254 in 151,724 control chromosomes in the GnomAD database, including 8,495 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 0.25 (8495 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0840
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 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: 0.253 AC: 38392 AN: 151606 Hom.: 8476 Cov.: 32

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.0713

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.0912

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0894

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.254 AC: 38464 AN: 151724 Hom.: 8495 Cov.: 32 AF XY: 0.254 AC XY: 18799 AN XY: 74120

African (AFR) AF: 0.567 AC: 23424 AN: 41336

American (AMR) AF: 0.168 AC: 2551 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3464

East Asian (EAS) AF: 0.585 AC: 3008 AN: 5140

South Asian (SAS) AF: 0.283 AC: 1358 AN: 4800

European-Finnish (FIN) AF: 0.0912 AC: 963 AN: 10554

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.0894 AC: 6072 AN: 67886

Other (OTH) AF: 0.210 AC: 443 AN: 2114

Alfa AF: 0.151 Hom.: 5725

Bravo AF: 0.275

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.25
PhyloP100		-0.084

Splicing

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

Other links and lift over

dbSNP: rs10908703; hg19: chr1-159252002;