rs10494654

Variant names:

• chr1-191522143-G-A
• rs10494654

Your query was ambiguous. Multiple possible variants found:

• chr1-191522143-G-A
• chr1-191522143-G-C

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 0.199 in 151,856 control chromosomes in the GnomAD database, including 4,220 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 0.20 (4220 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0560
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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: 0.199 AC: 30120 AN: 151738 Hom.: 4199 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.0607

Gnomad EAS AF: 0.0902

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.199 AC: 30187 AN: 151856 Hom.: 4220 Cov.: 32 AF XY: 0.201 AC XY: 14886 AN XY: 74244

African (AFR) AF: 0.383 AC: 15846 AN: 41410

American (AMR) AF: 0.242 AC: 3691 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.0607 AC: 210 AN: 3462

East Asian (EAS) AF: 0.0898 AC: 465 AN: 5178

South Asian (SAS) AF: 0.135 AC: 651 AN: 4820

European-Finnish (FIN) AF: 0.144 AC: 1520 AN: 10570

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7236 AN: 67870

Other (OTH) AF: 0.170 AC: 357 AN: 2098

Alfa AF: 0.120 Hom.: 1149

Bravo AF: 0.216

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		-0.056

Splicing

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

Other links and lift over

dbSNP: rs10494654; hg19: chr1-191491273;