rs10495179

Variant names:

• chr1-221796026-C-T
• rs10495179

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 0.138 in 151,492 control chromosomes in the GnomAD database, including 1,811 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 0.14 (1811 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.231 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: 0.138 AC: 20851 AN: 151372 Hom.: 1809 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0837

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0485

Gnomad EAS AF: 0.0827

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.138 AC: 20874 AN: 151492 Hom.: 1811 Cov.: 31 AF XY: 0.140 AC XY: 10348 AN XY: 74006

African (AFR) AF: 0.235 AC: 9696 AN: 41236

American (AMR) AF: 0.138 AC: 2102 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.0485 AC: 168 AN: 3466

East Asian (EAS) AF: 0.0823 AC: 423 AN: 5138

South Asian (SAS) AF: 0.0644 AC: 309 AN: 4798

European-Finnish (FIN) AF: 0.146 AC: 1525 AN: 10428

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.0925 AC: 6282 AN: 67898

Other (OTH) AF: 0.122 AC: 256 AN: 2102

Alfa AF: 0.115 Hom.: 210

Bravo AF: 0.143

Asia WGS AF: 0.0920 AC: 323 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10495179; hg19: chr1-221969368;