rs7127037

Variant names:

• chr11-130053128-T-A
• rs7127037

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 0.06 in 152,274 control chromosomes in the GnomAD database, including 268 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 0.060 (268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.574
• Publications: 1 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 (AFR) allele frequency at 95% confidence interval = 0.0789 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: 0.0600 AC: 9126 AN: 152156 Hom.: 268 Cov.: 32

Gnomad AFR AF: 0.0812

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.0416

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.0685

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0572

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0600 AC: 9141 AN: 152274 Hom.: 268 Cov.: 32 AF XY: 0.0587 AC XY: 4374 AN XY: 74460

African (AFR) AF: 0.0812 AC: 3374 AN: 41538

American (AMR) AF: 0.0415 AC: 635 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5192

South Asian (SAS) AF: 0.0180 AC: 87 AN: 4828

European-Finnish (FIN) AF: 0.0685 AC: 726 AN: 10606

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0572 AC: 3892 AN: 68024

Other (OTH) AF: 0.0515 AC: 109 AN: 2116

Alfa AF: 0.0619 Hom.: 39

Bravo AF: 0.0586

Asia WGS AF: 0.0270 AC: 94 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	2.6
DANN	Benign	0.65
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs7127037; hg19: chr11-129923023;