rs4149621

Positions:

• chr12-6342395-T-C

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 0.152 in 152,214 control chromosomes in the GnomAD database, including 4,861 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (4861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.147

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 12-6342395-T-C is Benign according to our data. Variant chr12-6342395-T-C is described in ClinVar as [Benign]. Clinvar id is 669759.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 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: 0.152 AC: 23045 AN: 152096 Hom.: 4849 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0891

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.00311

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.00906

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.152 AC: 23098 AN: 152214 Hom.: 4861 Cov.: 32 AF XY: 0.150 AC XY: 11151 AN XY: 74426

Gnomad4 AFR AF: 0.470

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0392

Gnomad4 EAS AF: 0.0893

Gnomad4 SAS AF: 0.0377

Gnomad4 FIN AF: 0.00311

Gnomad4 NFE AF: 0.00903

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0498 Hom.: 997

Bravo AF: 0.174

Asia WGS AF: 0.0910 AC: 317 AN: 3478

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

Jun 14, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.9
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4149621; hg19: chr12-6451561;