rs3129269

Variant names:

• chr6-33129837-C-A
• rs3129269
• ENST00000782892.1:n.430-11284C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-33129837-C-A
• chr6-33129837-C-G
• chr6-33129837-C-T

Variant summary

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

The ENST00000782892.1(ENSG00000291111):​n.430-11284C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,030 control chromosomes in the GnomAD database, including 7,306 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 0.31 (7306 hom., cov: 32)
• Consequence: ENSG00000291111 ENST00000782892.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 36 publications found

Genes affected

ENSG00000291111 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.525 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
ENSG00000291111	ENST00000782892.1	n.430-11284C>A		intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782893.1	n.404-11284C>A		intron_variant	Intron 2 of 2
ENSG00000291111	ENST00000782894.1	n.228+1093C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.305 AC: 46390 AN: 151914 Hom.: 7307 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.408

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.305 AC: 46407 AN: 152030 Hom.: 7306 Cov.: 32 AF XY: 0.307 AC XY: 22786 AN XY: 74290

African (AFR) AF: 0.253 AC: 10469 AN: 41448

American (AMR) AF: 0.252 AC: 3849 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.408 AC: 1414 AN: 3468

East Asian (EAS) AF: 0.242 AC: 1250 AN: 5160

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4818

European-Finnish (FIN) AF: 0.282 AC: 2971 AN: 10552

Middle Eastern (MID) AF: 0.411 AC: 120 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22735 AN: 67976

Other (OTH) AF: 0.311 AC: 658 AN: 2116

Alfa AF: 0.317 Hom.: 25084

Bravo AF: 0.294

Asia WGS AF: 0.373 AC: 1296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.28
DANN	Benign	0.20
PhyloP100		0.045

Splicing

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

Other links and lift over

dbSNP: rs3129269; hg19: chr6-33097614;