11-93636139-C-A

Variant names:

• chr11-93636139-C-A
• rs948016

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 0.414 in 151,986 control chromosomes in the GnomAD database, including 14,023 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 0.41 (14023 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.533
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.552 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: 0.414 AC: 62847 AN: 151868 Hom.: 14013 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.561

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.469

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.414 AC: 62869 AN: 151986 Hom.: 14023 Cov.: 33 AF XY: 0.416 AC XY: 30892 AN XY: 74272

African (AFR) AF: 0.247 AC: 10242 AN: 41480

American (AMR) AF: 0.562 AC: 8575 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3470

East Asian (EAS) AF: 0.470 AC: 2414 AN: 5140

South Asian (SAS) AF: 0.494 AC: 2383 AN: 4820

European-Finnish (FIN) AF: 0.416 AC: 4392 AN: 10558

Middle Eastern (MID) AF: 0.415 AC: 122 AN: 294

European-Non Finnish (NFE) AF: 0.464 AC: 31509 AN: 67936

Other (OTH) AF: 0.408 AC: 861 AN: 2112

Alfa AF: 0.463 Hom.: 10734

Bravo AF: 0.418

Asia WGS AF: 0.442 AC: 1538 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.6
DANN	Benign	0.67
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs948016; hg19: chr11-93369305;