rs2110041

Variant names:

• chr1-187912463-T-C
• rs2110041

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 0.145 in 152,226 control chromosomes in the GnomAD database, including 1,867 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 (1867 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22070 AN: 152108 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.0601

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.145 AC: 22067 AN: 152226 Hom.: 1867 Cov.: 32 AF XY: 0.146 AC XY: 10875 AN XY: 74432

African (AFR) AF: 0.0600 AC: 2495 AN: 41560

American (AMR) AF: 0.122 AC: 1866 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3472

East Asian (EAS) AF: 0.102 AC: 530 AN: 5174

South Asian (SAS) AF: 0.300 AC: 1447 AN: 4816

European-Finnish (FIN) AF: 0.188 AC: 1988 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12619 AN: 68010

Other (OTH) AF: 0.163 AC: 345 AN: 2112

Alfa AF: 0.155 Hom.: 337

Bravo AF: 0.132

Asia WGS AF: 0.193 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.7
DANN	Benign	0.40
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs2110041; hg19: chr1-187881594;