rs10494027

Variant names:

• chr1-105188577-G-A
• rs10494027

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 0.0528 in 152,052 control chromosomes in the GnomAD database, including 547 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 0.053 (547 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.458
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.25 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: 0.0528 AC: 8020 AN: 151934 Hom.: 546 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.0795

Gnomad FIN AF: 0.00350

Gnomad MID AF: 0.0392

Gnomad NFE AF: 0.00968

Gnomad OTH AF: 0.0435

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

GnomAD4 genome AF: 0.0528 AC: 8027 AN: 152052 Hom.: 547 Cov.: 32 AF XY: 0.0529 AC XY: 3930 AN XY: 74342

African (AFR) AF: 0.120 AC: 4979 AN: 41480

American (AMR) AF: 0.0312 AC: 476 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0130 AC: 45 AN: 3472

East Asian (EAS) AF: 0.261 AC: 1351 AN: 5170

South Asian (SAS) AF: 0.0785 AC: 379 AN: 4826

European-Finnish (FIN) AF: 0.00350 AC: 37 AN: 10584

Middle Eastern (MID) AF: 0.0385 AC: 11 AN: 286

European-Non Finnish (NFE) AF: 0.00969 AC: 658 AN: 67940

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0364 Hom.: 52

Bravo AF: 0.0582

Asia WGS AF: 0.152 AC: 522 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.6
DANN	Benign	0.33
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs10494027; hg19: chr1-105731199;