rs1857063

Positions:

• chr10-29041086-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 109 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00755

Gnomad4 AMR AF: 0.0296

Gnomad4 ASJ AF: 0.0516

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0130

Gnomad4 FIN AF: 0.0650

Gnomad4 NFE AF: 0.0460

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0427 Hom.: 20

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1857063; hg19: chr10-29330015;