1-181076285-C-T

Variant names:

• chr1-181076285-C-T
• rs10910862

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.129 in 152,158 control chromosomes in the GnomAD database, including 1,934 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 0.13 (1934 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.27 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: 0.129 AC: 19606 AN: 152040 Hom.: 1926 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0515

Gnomad AMR AF: 0.0828

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0621

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.0649

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.129 AC: 19644 AN: 152158 Hom.: 1934 Cov.: 32 AF XY: 0.125 AC XY: 9289 AN XY: 74372

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0619

Gnomad4 SAS AF: 0.0575

Gnomad4 FIN AF: 0.0649

Gnomad4 NFE AF: 0.0739

Gnomad4 OTH AF: 0.114

Alfa AF: 0.0761 Hom.: 524

Bravo AF: 0.139

Asia WGS AF: 0.0740 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10910862; hg19: chr1-181045421;