rs3814759

Positions:

• chr11-119346870-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.581 in 151,684 control chromosomes in the GnomAD database, including 25,763 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.58 (25763 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -4.53

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 11-119346870-C-T is Benign according to our data. Variant chr11-119346870-C-T is described in ClinVar as [Benign]. Clinvar id is 1250347.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 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: 0.581 AC: 88074 AN: 151566 Hom.: 25737 Cov.: 34

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.711

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.581 AC: 88145 AN: 151684 Hom.: 25763 Cov.: 34 AF XY: 0.583 AC XY: 43236 AN XY: 74156

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.544

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.604

Alfa AF: 0.579 Hom.: 3791

Bravo AF: 0.583

Asia WGS AF: 0.714 AC: 2481 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.51
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3814759; hg19: chr11-119217580;