rs10908703

Positions:

• chr1-159282212-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 0.254 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.253 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

Gnomad4 AFR AF: 0.567

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.585

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.0912

Gnomad4 NFE AF: 0.0894

Gnomad4 OTH AF: 0.210

Alfa AF: 0.163 Hom.: 1635

Bravo AF: 0.275

Asia WGS AF: 0.389 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10908703; hg19: chr1-159252002;