11-4094428-T-G

Variant names:

• chr11-4094428-T-G
• rs1735068

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 0.799 in 152,244 control chromosomes in the GnomAD database, including 50,832 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 0.80 (50832 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.806
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.923 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: 0.799 AC: 121605 AN: 152126 Hom.: 50835 Cov.: 34

Gnomad AFR AF: 0.536

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.756

Gnomad SAS AF: 0.934

Gnomad FIN AF: 0.888

Gnomad MID AF: 0.823

Gnomad NFE AF: 0.929

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.799 AC: 121640 AN: 152244 Hom.: 50832 Cov.: 34 AF XY: 0.800 AC XY: 59549 AN XY: 74456

African (AFR) AF: 0.536 AC: 22219 AN: 41490

American (AMR) AF: 0.819 AC: 12531 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3162 AN: 3472

East Asian (EAS) AF: 0.755 AC: 3908 AN: 5176

South Asian (SAS) AF: 0.934 AC: 4509 AN: 4828

European-Finnish (FIN) AF: 0.888 AC: 9428 AN: 10614

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.929 AC: 63202 AN: 68038

Other (OTH) AF: 0.809 AC: 1710 AN: 2114

Alfa AF: 0.818 Hom.: 4037

Bravo AF: 0.775

Asia WGS AF: 0.782 AC: 2720 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.1
DANN	Benign	0.48
PhyloP100		-0.81
PromoterAI		0.030	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1735068; hg19: chr11-4115658;