rs4077759

Variant names:

• chr11-1112068-C-T
• rs4077759

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 0.539 in 151,840 control chromosomes in the GnomAD database, including 23,735 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 0.54 (23735 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.92
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.647 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: 0.539 AC: 81831 AN: 151722 Hom.: 23748 Cov.: 32

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.701

Gnomad EAS AF: 0.667

Gnomad SAS AF: 0.639

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.663

Gnomad NFE AF: 0.631

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.539 AC: 81834 AN: 151840 Hom.: 23735 Cov.: 32 AF XY: 0.541 AC XY: 40169 AN XY: 74208

African (AFR) AF: 0.313 AC: 12964 AN: 41422

American (AMR) AF: 0.539 AC: 8210 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.701 AC: 2427 AN: 3464

East Asian (EAS) AF: 0.666 AC: 3433 AN: 5154

South Asian (SAS) AF: 0.638 AC: 3071 AN: 4810

European-Finnish (FIN) AF: 0.640 AC: 6756 AN: 10560

Middle Eastern (MID) AF: 0.669 AC: 194 AN: 290

European-Non Finnish (NFE) AF: 0.631 AC: 42826 AN: 67890

Other (OTH) AF: 0.567 AC: 1196 AN: 2108

Alfa AF: 0.604 Hom.: 80962

Bravo AF: 0.522

Asia WGS AF: 0.597 AC: 2076 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.3
DANN	Benign	0.34
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs4077759; hg19: chr11-1105976;