rs4938285

Variant names:

• chr11-116569294-T-C
• rs4938285

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 0.361 in 151,896 control chromosomes in the GnomAD database, including 10,277 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 0.36 (10277 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.35
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.443 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: 0.361 AC: 54798 AN: 151776 Hom.: 10264 Cov.: 31

Gnomad AFR AF: 0.448

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.293

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.361 AC: 54855 AN: 151896 Hom.: 10277 Cov.: 31 AF XY: 0.353 AC XY: 26227 AN XY: 74224

African (AFR) AF: 0.448 AC: 18547 AN: 41372

American (AMR) AF: 0.293 AC: 4478 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1232 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1635 AN: 5146

South Asian (SAS) AF: 0.342 AC: 1648 AN: 4812

European-Finnish (FIN) AF: 0.214 AC: 2252 AN: 10542

Middle Eastern (MID) AF: 0.377 AC: 110 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23896 AN: 67964

Other (OTH) AF: 0.368 AC: 778 AN: 2114

Alfa AF: 0.354 Hom.: 1978

Bravo AF: 0.368

Asia WGS AF: 0.309 AC: 1075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	20
DANN	Benign	0.67
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs4938285; hg19: chr11-116440011;