rs10908474

Variant names:

• chr1-153781249-C-A
• rs10908474

Your query was ambiguous. Multiple possible variants found:

• chr1-153781249-C-A
• chr1-153781249-C-G
• chr1-153781249-C-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 0.342 in 151,974 control chromosomes in the GnomAD database, including 9,268 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 0.34 (9268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.12
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.421 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: 0.342 AC: 51951 AN: 151856 Hom.: 9272 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.342 AC: 51967 AN: 151974 Hom.: 9268 Cov.: 32 AF XY: 0.345 AC XY: 25588 AN XY: 74260

African (AFR) AF: 0.230 AC: 9558 AN: 41472

American (AMR) AF: 0.430 AC: 6563 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1216 AN: 3468

East Asian (EAS) AF: 0.328 AC: 1691 AN: 5162

South Asian (SAS) AF: 0.397 AC: 1914 AN: 4818

European-Finnish (FIN) AF: 0.378 AC: 3984 AN: 10544

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.379 AC: 25769 AN: 67944

Other (OTH) AF: 0.368 AC: 775 AN: 2104

Alfa AF: 0.368 Hom.: 13910

Bravo AF: 0.345

Asia WGS AF: 0.370 AC: 1286 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.015
DANN	Benign	0.37
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs10908474; hg19: chr1-153753725;