rs10494655

Variant names:

• chr1-191658617-T-A
• rs10494655

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 0.0603 in 152,182 control chromosomes in the GnomAD database, including 423 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 0.060 (423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.118 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: 0.0602 AC: 9160 AN: 152064 Hom.: 422 Cov.: 32

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0415

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.0602

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0298

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0603 AC: 9175 AN: 152182 Hom.: 423 Cov.: 32 AF XY: 0.0609 AC XY: 4530 AN XY: 74382

African (AFR) AF: 0.121 AC: 5020 AN: 41514

American (AMR) AF: 0.0472 AC: 721 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0415 AC: 144 AN: 3468

East Asian (EAS) AF: 0.109 AC: 564 AN: 5162

South Asian (SAS) AF: 0.0604 AC: 291 AN: 4816

European-Finnish (FIN) AF: 0.0236 AC: 251 AN: 10622

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0298 AC: 2028 AN: 68016

Other (OTH) AF: 0.0596 AC: 126 AN: 2114

Alfa AF: 0.0149 Hom.: 8

Bravo AF: 0.0649

Asia WGS AF: 0.0980 AC: 340 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.7
DANN	Benign	0.38
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs10494655; hg19: chr1-191627747;