rs4754752

Variant names:

• chr11-101354999-T-C
• rs4754752

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 0.247 in 152,144 control chromosomes in the GnomAD database, including 4,833 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 0.25 (4833 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 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: 0.246 AC: 37471 AN: 152026 Hom.: 4811 Cov.: 32

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.259

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

GnomAD4 genome AF: 0.247 AC: 37546 AN: 152144 Hom.: 4833 Cov.: 32 AF XY: 0.250 AC XY: 18622 AN XY: 74380

African (AFR) AF: 0.288 AC: 11945 AN: 41516

American (AMR) AF: 0.296 AC: 4519 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3472

East Asian (EAS) AF: 0.394 AC: 2030 AN: 5156

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4816

European-Finnish (FIN) AF: 0.212 AC: 2243 AN: 10596

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13994 AN: 67986

Other (OTH) AF: 0.266 AC: 562 AN: 2114

Alfa AF: 0.231 Hom.: 1628

Bravo AF: 0.253

Asia WGS AF: 0.293 AC: 1018 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.15
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4754752; hg19: chr11-101225730;