rs4754011

Variant names:

• chr11-97071393-G-A
• rs4754011

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 0.203 in 151,432 control chromosomes in the GnomAD database, including 3,388 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 0.20 (3388 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.455 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: 0.203 AC: 30766 AN: 151312 Hom.: 3391 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.203 AC: 30791 AN: 151432 Hom.: 3388 Cov.: 31 AF XY: 0.208 AC XY: 15359 AN XY: 73954

African (AFR) AF: 0.173 AC: 7128 AN: 41310

American (AMR) AF: 0.249 AC: 3788 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3462

East Asian (EAS) AF: 0.471 AC: 2406 AN: 5108

South Asian (SAS) AF: 0.279 AC: 1344 AN: 4812

European-Finnish (FIN) AF: 0.159 AC: 1649 AN: 10368

Middle Eastern (MID) AF: 0.247 AC: 72 AN: 292

European-Non Finnish (NFE) AF: 0.192 AC: 13027 AN: 67830

Other (OTH) AF: 0.205 AC: 431 AN: 2098

Alfa AF: 0.196 Hom.: 4007

Bravo AF: 0.207

Asia WGS AF: 0.356 AC: 1235 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.5
DANN	Benign	0.30
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs4754011; hg19: chr11-96942393;