rs4129284

Variant names:

• chr6-132581276-C-T
• rs4129284

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.531 in 151,956 control chromosomes in the GnomAD database, including 22,090 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (22090 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.147
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.557 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: 80682 AN: 151838 Hom.: 22071 Cov.: 32

Gnomad AFR AF: 0.563

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.455

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.531 AC: 80749 AN: 151956 Hom.: 22090 Cov.: 32 AF XY: 0.526 AC XY: 39097 AN XY: 74260

African (AFR) AF: 0.563 AC: 23320 AN: 41440

American (AMR) AF: 0.455 AC: 6941 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.455 AC: 1577 AN: 3464

East Asian (EAS) AF: 0.208 AC: 1071 AN: 5148

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4812

European-Finnish (FIN) AF: 0.618 AC: 6520 AN: 10552

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37964 AN: 67974

Other (OTH) AF: 0.493 AC: 1038 AN: 2104

Alfa AF: 0.556 Hom.: 4902

Bravo AF: 0.520

Asia WGS AF: 0.312 AC: 1088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.55
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs4129284; hg19: chr6-132902415;