6-29643654-C-T

Variant names:

• chr6-29643654-C-T
• rs29232
• ENST00000782059.1:n.436-7464G>A

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.436-7464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,918 control chromosomes in the GnomAD database, including 12,411 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 0.39 (12411 hom., cov: 32)
• Consequence: ENSG00000301820 ENST00000782059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412
• Publications: 65 publications found

Genes affected

ENSG00000301820 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000782059.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000301820	ENST00000782059.1		n.436-7464G>A		intron	N/A
	ENSG00000301820	ENST00000782060.1		n.432-7464G>A		intron	N/A
	ENSG00000301820	ENST00000782061.1		n.312-7464G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59606 AN: 151800 Hom.: 12387 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.520

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.659

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.393 AC: 59677 AN: 151918 Hom.: 12411 Cov.: 32 AF XY: 0.396 AC XY: 29424 AN XY: 74236

African (AFR) AF: 0.367 AC: 15218 AN: 41420

American (AMR) AF: 0.521 AC: 7953 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1819 AN: 3470

East Asian (EAS) AF: 0.511 AC: 2627 AN: 5144

South Asian (SAS) AF: 0.659 AC: 3174 AN: 4820

European-Finnish (FIN) AF: 0.248 AC: 2616 AN: 10552

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.366 AC: 24876 AN: 67936

Other (OTH) AF: 0.450 AC: 950 AN: 2110

Alfa AF: 0.385 Hom.: 46605

Bravo AF: 0.405

Asia WGS AF: 0.627 AC: 2182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.6
DANN	Benign	0.90
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs29232; hg19: chr6-29611431;