rs2110041

chr1-187912463-T-C

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 0.145 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.0600

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.300

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.163

Alfa AF: 0.158 Hom.: 334

Bravo AF: 0.132

Asia WGS AF: 0.193 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.7
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2110041; hg19: chr1-187881594;