rs1857063

Variant names:

• chr10-29041086-G-A
• rs1857063

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0324 in 152,300 control chromosomes in the GnomAD database, including 109 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 0.032 (109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0324 (4936/152300) while in subpopulation NFE AF = 0.046 (3129/68028). AF 95% confidence interval is 0.0447. There are 109 homozygotes in GnomAd4. There are 2461 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 109 gene

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: 0.0325 AC: 4939 AN: 152182 Hom.: 109 Cov.: 32

Gnomad AFR AF: 0.00758

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0296

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0132

Gnomad FIN AF: 0.0650

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0460

Gnomad OTH AF: 0.0353

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

GnomAD4 genome AF: 0.0324 AC: 4936 AN: 152300 Hom.: 109 Cov.: 32 AF XY: 0.0331 AC XY: 2461 AN XY: 74456

African (AFR) AF: 0.00755 AC: 314 AN: 41572

American (AMR) AF: 0.0296 AC: 453 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5188

South Asian (SAS) AF: 0.0130 AC: 63 AN: 4828

European-Finnish (FIN) AF: 0.0650 AC: 688 AN: 10590

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0460 AC: 3129 AN: 68028

Other (OTH) AF: 0.0350 AC: 74 AN: 2116

Alfa AF: 0.0432 Hom.: 46

Bravo AF: 0.0280

Asia WGS AF: 0.00462 AC: 16 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.61
DANN	Benign	0.37
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1857063; hg19: chr10-29330015;