rs10494825

Variant names:

• chr1-200504351-C-T
• rs10494825

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 0.183 in 151,830 control chromosomes in the GnomAD database, including 3,278 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 0.18 (3278 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.271 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: 0.183 AC: 27752 AN: 151712 Hom.: 3275 Cov.: 31

Gnomad AFR AF: 0.0502

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.183 AC: 27750 AN: 151830 Hom.: 3278 Cov.: 31 AF XY: 0.175 AC XY: 12979 AN XY: 74218

African (AFR) AF: 0.0501 AC: 2077 AN: 41480

American (AMR) AF: 0.166 AC: 2533 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.338 AC: 1173 AN: 3470

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5176

South Asian (SAS) AF: 0.173 AC: 836 AN: 4822

European-Finnish (FIN) AF: 0.171 AC: 1790 AN: 10466

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.274 AC: 18588 AN: 67848

Other (OTH) AF: 0.215 AC: 452 AN: 2106

Alfa AF: 0.247 Hom.: 2746

Bravo AF: 0.176

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.44
PhyloP100		0.022

Splicing

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

Other links and lift over

dbSNP: rs10494825; hg19: chr1-200473479;