rs10801805

Variant names:

• chr1-90354699-G-A
• rs10801805

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 0.39 in 152,076 control chromosomes in the GnomAD database, including 11,716 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 0.39 (11716 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.782
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.528 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: 0.390 AC: 59256 AN: 151958 Hom.: 11679 Cov.: 33

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.369

Gnomad EAS AF: 0.545

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.390 AC: 59342 AN: 152076 Hom.: 11716 Cov.: 33 AF XY: 0.392 AC XY: 29154 AN XY: 74342

African (AFR) AF: 0.447 AC: 18530 AN: 41490

American (AMR) AF: 0.330 AC: 5043 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.369 AC: 1282 AN: 3470

East Asian (EAS) AF: 0.545 AC: 2820 AN: 5174

South Asian (SAS) AF: 0.454 AC: 2187 AN: 4812

European-Finnish (FIN) AF: 0.393 AC: 4156 AN: 10570

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24377 AN: 67968

Other (OTH) AF: 0.358 AC: 755 AN: 2110

Alfa AF: 0.368 Hom.: 8313

Bravo AF: 0.383

Asia WGS AF: 0.520 AC: 1806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.30
DANN	Benign	0.69
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs10801805; hg19: chr1-90820257;