rs7127037

chr11-130053128-T-A

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 0.06 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

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 (AFR) allele frequency at 95% confidence interval = 0.0789 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: 0.0600 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

Gnomad4 AFR AF: 0.0812

Gnomad4 AMR AF: 0.0415

Gnomad4 ASJ AF: 0.0637

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0180

Gnomad4 FIN AF: 0.0685

Gnomad4 NFE AF: 0.0572

Gnomad4 OTH AF: 0.0515

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7127037; hg19: chr11-129923023;