rs7965413

Variant names:

• chr12-6125723-C-T
• rs7965413

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 0.531 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, single submitter B:2
• Conservation: PhyloP100: -3.15

ACMG classification

Verdict is Benign. Variant got -14 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_single_submitter, 1 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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, single submitter

Submissions by phenotype

not provided Benign:1

Apr 12, 2018

Quest Diagnostics Nichols Institute San Juan Capistrano

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

VWF-related disorder Benign:1

Mar 05, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

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;