rs1885301

Variant names:

• chr10-99781296-A-G
• rs1885301

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 0.58 in 151,910 control chromosomes in the GnomAD database, including 25,807 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 0.58 (25807 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.234
• Publications: 39 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.75 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: 0.580 AC: 88005 AN: 151792 Hom.: 25794 Cov.: 31

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.527

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.580 AC: 88065 AN: 151910 Hom.: 25807 Cov.: 31 AF XY: 0.584 AC XY: 43357 AN XY: 74284

African (AFR) AF: 0.564 AC: 23338 AN: 41406

American (AMR) AF: 0.567 AC: 8656 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.527 AC: 1827 AN: 3470

East Asian (EAS) AF: 0.770 AC: 3974 AN: 5164

South Asian (SAS) AF: 0.625 AC: 3011 AN: 4818

European-Finnish (FIN) AF: 0.636 AC: 6706 AN: 10536

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38835 AN: 67936

Other (OTH) AF: 0.546 AC: 1153 AN: 2110

Alfa AF: 0.580 Hom.: 42810

Bravo AF: 0.575

Asia WGS AF: 0.658 AC: 2284 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.63
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1885301; hg19: chr10-101541053;