rs4149621

Variant names:

• chr12-6342395-T-C
• rs4149621

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 0.152 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.470 AC: 19496 AN: 41492

American (AMR) AF: 0.122 AC: 1858 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3472

East Asian (EAS) AF: 0.0893 AC: 462 AN: 5176

South Asian (SAS) AF: 0.0377 AC: 182 AN: 4826

European-Finnish (FIN) AF: 0.00311 AC: 33 AN: 10616

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.00903 AC: 614 AN: 68020

Other (OTH) AF: 0.128 AC: 271 AN: 2114

Alfa AF: 0.0556 Hom.: 1292

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

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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
PhyloP100		0.15
PromoterAI		0.0031	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4149621; hg19: chr12-6451561;