rs7965413

Positions:

• chr12-6125723-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.531 in 151,926 control chromosomes in the GnomAD database, including 22,433 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.53 (22433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -3.15

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.07).
• BP6: Variant 12-6125723-C-T is Benign according to our data. Variant chr12-6125723-C-T is described in ClinVar as [Benign]. Clinvar id is 619927.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80618 AN: 151808 Hom.: 22433 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.534

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

GnomAD4 genome AF: 0.531 AC: 80633 AN: 151926 Hom.: 22433 Cov.: 32 AF XY: 0.525 AC XY: 39008 AN XY: 74268

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.477

Gnomad4 ASJ AF: 0.503

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.527

Alfa AF: 0.583 Hom.: 3293

Bravo AF: 0.515

Asia WGS AF: 0.417 AC: 1454 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Apr 12, 2018

- -

VWF-related disorder Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 05, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7965413; hg19: chr12-6234889;