11-128871185-T-C

Variant names:

• chr11-128871185-T-C
• rs4529890

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 0.883 in 152,238 control chromosomes in the GnomAD database, including 59,497 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 0.88 (59497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.144
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.883 AC: 134360 AN: 152120 Hom.: 59451 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.900

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.890

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.857

Gnomad OTH AF: 0.881

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

GnomAD4 genome AF: 0.883 AC: 134461 AN: 152238 Hom.: 59497 Cov.: 32 AF XY: 0.881 AC XY: 65599 AN XY: 74438

African (AFR) AF: 0.938 AC: 38971 AN: 41554

American (AMR) AF: 0.912 AC: 13959 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.898 AC: 3114 AN: 3466

East Asian (EAS) AF: 0.890 AC: 4603 AN: 5174

South Asian (SAS) AF: 0.749 AC: 3612 AN: 4822

European-Finnish (FIN) AF: 0.844 AC: 8948 AN: 10600

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.857 AC: 58309 AN: 68002

Other (OTH) AF: 0.880 AC: 1863 AN: 2116

Alfa AF: 0.877 Hom.: 15784

Bravo AF: 0.892

Asia WGS AF: 0.829 AC: 2886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.7
DANN	Benign	0.87
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs4529890; hg19: chr11-128741080;