rs10888394

Variant names:

• chr1-150777437-C-T
• rs10888394

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 0.355 in 151,948 control chromosomes in the GnomAD database, including 9,925 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 0.35 (9925 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.523 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: 0.355 AC: 53865 AN: 151830 Hom.: 9917 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.355 AC: 53885 AN: 151948 Hom.: 9925 Cov.: 32 AF XY: 0.360 AC XY: 26743 AN XY: 74252

African (AFR) AF: 0.277 AC: 11463 AN: 41422

American (AMR) AF: 0.419 AC: 6396 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1664 AN: 3470

East Asian (EAS) AF: 0.391 AC: 2021 AN: 5170

South Asian (SAS) AF: 0.540 AC: 2602 AN: 4818

European-Finnish (FIN) AF: 0.348 AC: 3667 AN: 10534

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.367 AC: 24926 AN: 67950

Other (OTH) AF: 0.370 AC: 782 AN: 2112

Alfa AF: 0.362 Hom.: 15995

Bravo AF: 0.350

Asia WGS AF: 0.414 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	12
DANN	Benign	0.72
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs10888394; hg19: chr1-150749913; COSMIC: COSV51616628;