rs2511211

Variant names:

• chr1-159260681-T-G
• rs2511211

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 0.149 in 152,264 control chromosomes in the GnomAD database, including 2,347 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 0.15 (2347 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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: 0.149 AC: 22725 AN: 152146 Hom.: 2347 Cov.: 33

Gnomad AFR AF: 0.0382

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.0796

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.227

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.149 AC: 22720 AN: 152264 Hom.: 2347 Cov.: 33 AF XY: 0.147 AC XY: 10939 AN XY: 74448

African (AFR) AF: 0.0381 AC: 1583 AN: 41588

American (AMR) AF: 0.119 AC: 1823 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0796 AC: 276 AN: 3466

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.119 AC: 576 AN: 4830

European-Finnish (FIN) AF: 0.227 AC: 2409 AN: 10594

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15608 AN: 67976

Other (OTH) AF: 0.149 AC: 316 AN: 2114

Alfa AF: 0.188 Hom.: 438

Bravo AF: 0.135

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	8.0
DANN	Benign	0.33
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs2511211; hg19: chr1-159230471;