rs4077759

Positions:

• chr11-1112068-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.313

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.701

Gnomad4 EAS AF: 0.666

Gnomad4 SAS AF: 0.638

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.631

Gnomad4 OTH AF: 0.567

Alfa AF: 0.620 Hom.: 38193

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4077759; hg19: chr11-1105976;