rs10494029

Variant names:

• chr1-105431244-T-A
• rs10494029

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 0.0231 in 152,036 control chromosomes in the GnomAD database, including 62 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 0.023 (62 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.0231 (3518/152036) while in subpopulation AMR AF = 0.0375 (572/15256). AF 95% confidence interval is 0.035. There are 62 homozygotes in GnomAd4. There are 1707 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 62 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: 0.0232 AC: 3522 AN: 151920 Hom.: 63 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0197

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0231 AC: 3518 AN: 152036 Hom.: 62 Cov.: 33 AF XY: 0.0230 AC XY: 1707 AN XY: 74336

African (AFR) AF: 0.0291 AC: 1210 AN: 41532

American (AMR) AF: 0.0375 AC: 572 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0433 AC: 150 AN: 3464

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0184 AC: 89 AN: 4826

European-Finnish (FIN) AF: 0.00245 AC: 26 AN: 10616

Middle Eastern (MID) AF: 0.124 AC: 36 AN: 290

European-Non Finnish (NFE) AF: 0.0197 AC: 1338 AN: 67858

Other (OTH) AF: 0.0332 AC: 70 AN: 2108

Alfa AF: 0.0207 Hom.: 8

Bravo AF: 0.0269

Asia WGS AF: 0.0100 AC: 35 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.67
PhyloP100		0.085

Splicing

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

Other links and lift over

dbSNP: rs10494029; hg19: chr1-105973866;