rs7128311

Variant names:

• chr11-20540973-C-T
• rs7128311

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 0.969 in 152,312 control chromosomes in the GnomAD database, including 72,006 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 0.97 (72006 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.102

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.970 AC: 147556 AN: 152194 Hom.: 71957 Cov.: 32

Gnomad AFR AF: 0.994

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.899

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.966

Gnomad FIN AF: 0.975

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.995

Gnomad OTH AF: 0.965

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

GnomAD4 genome AF: 0.969 AC: 147663 AN: 152312 Hom.: 72006 Cov.: 32 AF XY: 0.966 AC XY: 71945 AN XY: 74470

Gnomad4 AFR AF: 0.994

Gnomad4 AMR AF: 0.898

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.966

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.995

Gnomad4 OTH AF: 0.965

Alfa AF: 0.973 Hom.: 86306

Bravo AF: 0.959

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7128311; hg19: chr11-20562519;