11-128278233-A-T

Variant names:

• chr11-128278233-A-T
• rs510628

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 0.93 in 152,282 control chromosomes in the GnomAD database, including 65,954 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 0.93 (65954 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.956 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: 0.930 AC: 141462 AN: 152164 Hom.: 65910 Cov.: 32

Gnomad AFR AF: 0.873

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.890

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.955

Gnomad FIN AF: 0.955

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.962

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.930 AC: 141563 AN: 152282 Hom.: 65954 Cov.: 32 AF XY: 0.930 AC XY: 69273 AN XY: 74462

Gnomad4 AFR AF: 0.873

Gnomad4 AMR AF: 0.889

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.955

Gnomad4 FIN AF: 0.955

Gnomad4 NFE AF: 0.962

Gnomad4 OTH AF: 0.930

Alfa AF: 0.945 Hom.: 8442

Bravo AF: 0.918

Asia WGS AF: 0.934 AC: 3243 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
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: rs510628; hg19: chr11-128148128;