rs10494737

Variant names:

• chr1-195893729-C-T
• rs10494737

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 0.248 in 151,866 control chromosomes in the GnomAD database, including 4,884 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 0.25 (4884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.336 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: 0.248 AC: 37688 AN: 151748 Hom.: 4882 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.253

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.350

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.248 AC: 37698 AN: 151866 Hom.: 4884 Cov.: 32 AF XY: 0.251 AC XY: 18604 AN XY: 74226

African (AFR) AF: 0.181 AC: 7501 AN: 41466

American (AMR) AF: 0.253 AC: 3865 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.234 AC: 808 AN: 3456

East Asian (EAS) AF: 0.350 AC: 1782 AN: 5096

South Asian (SAS) AF: 0.280 AC: 1350 AN: 4824

European-Finnish (FIN) AF: 0.318 AC: 3366 AN: 10586

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18090 AN: 67868

Other (OTH) AF: 0.239 AC: 505 AN: 2112

Alfa AF: 0.261 Hom.: 22365

Bravo AF: 0.241

Asia WGS AF: 0.280 AC: 979 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	5.0
DANN	Benign	0.87
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs10494737; hg19: chr1-195862859;