rs7965413

Variant names:

• chr12-6125723-C-T
• rs7965413

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.376 AC: 15566 AN: 41418

American (AMR) AF: 0.477 AC: 7277 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1745 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2057 AN: 5152

South Asian (SAS) AF: 0.462 AC: 2228 AN: 4822

European-Finnish (FIN) AF: 0.603 AC: 6359 AN: 10552

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.641 AC: 43574 AN: 67956

Other (OTH) AF: 0.527 AC: 1111 AN: 2108

Alfa AF: 0.583 Hom.: 3293

Bravo AF: 0.515

Asia WGS AF: 0.417 AC: 1454 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)
-	-	1	VWF-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.10
DANN	Benign	0.68
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs7965413; hg19: chr12-6234889;