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.

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: 0.152 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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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;