rs2071174

Variant names:

• chr11-1073712-T-C
• rs2071174

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 0.383 in 152,164 control chromosomes in the GnomAD database, including 11,909 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 0.38 (11909 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.65
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.515 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: 0.383 AC: 58201 AN: 152046 Hom.: 11897 Cov.: 34

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.383 AC: 58255 AN: 152164 Hom.: 11909 Cov.: 34 AF XY: 0.382 AC XY: 28456 AN XY: 74404

African (AFR) AF: 0.521 AC: 21621 AN: 41518

American (AMR) AF: 0.238 AC: 3638 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2405 AN: 5152

South Asian (SAS) AF: 0.206 AC: 994 AN: 4832

European-Finnish (FIN) AF: 0.433 AC: 4594 AN: 10612

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23019 AN: 67966

Other (OTH) AF: 0.326 AC: 688 AN: 2108

Alfa AF: 0.332 Hom.: 19174

Bravo AF: 0.375

Asia WGS AF: 0.335 AC: 1165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.37
DANN	Benign	0.83
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs2071174; hg19: chr11-1073712;