11-128455658-T-C

Variant names:

• chr11-128455658-T-C
• rs10893872

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 0.443 in 151,986 control chromosomes in the GnomAD database, including 16,113 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 0.44 (16113 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.547 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: 0.444 AC: 67361 AN: 151868 Hom.: 16113 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.575

Gnomad EAS AF: 0.564

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.443 AC: 67365 AN: 151986 Hom.: 16113 Cov.: 32 AF XY: 0.448 AC XY: 33246 AN XY: 74274

African (AFR) AF: 0.259 AC: 10726 AN: 41466

American (AMR) AF: 0.410 AC: 6264 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.575 AC: 1996 AN: 3470

East Asian (EAS) AF: 0.564 AC: 2915 AN: 5168

South Asian (SAS) AF: 0.552 AC: 2656 AN: 4812

European-Finnish (FIN) AF: 0.586 AC: 6170 AN: 10534

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35011 AN: 67946

Other (OTH) AF: 0.473 AC: 1000 AN: 2116

Alfa AF: 0.489 Hom.: 31698

Bravo AF: 0.423

Asia WGS AF: 0.574 AC: 1995 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.0
DANN	Benign	0.73
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10893872; hg19: chr11-128325553;