rs4980785

Positions:

• chr11-69419726-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 0.52 in 152,078 control chromosomes in the GnomAD database, including 22,119 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 0.52 (22119 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 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: 0.519 AC: 78939 AN: 151960 Hom.: 22061 Cov.: 33

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.527

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.350

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.520 AC: 79066 AN: 152078 Hom.: 22119 Cov.: 33 AF XY: 0.518 AC XY: 38532 AN XY: 74348

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.550

Gnomad4 ASJ AF: 0.350

Gnomad4 EAS AF: 0.510

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.446

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.467

Alfa AF: 0.426 Hom.: 19961

Bravo AF: 0.537

Asia WGS AF: 0.470 AC: 1636 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.2
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4980785; hg19: chr11-69234494;