6-29855829-A-G

Variant names:

• chr6-29855829-A-G
• rs3132726
• ENST00000647952.1:n.2155+1517T>C

Variant summary

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

The ENST00000647952.1(ENSG00000290870):​n.2155+1517T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.759 in 152,098 control chromosomes in the GnomAD database, including 43,934 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 0.76 (43934 hom., cov: 32)
• Consequence: ENSG00000290870 ENST00000647952.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.27
• Publications: 20 publications found

Genes affected

ENSG00000290870 (HGNC:59164):

LOC105375010 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647952.1. 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
	ENSG00000290870	ENST00000647952.1		n.2155+1517T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.759 AC: 115320 AN: 151978 Hom.: 43908 Cov.: 32

Gnomad AFR AF: 0.777

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.737

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.762

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.759 AC: 115398 AN: 152098 Hom.: 43934 Cov.: 32 AF XY: 0.753 AC XY: 56023 AN XY: 74378

African (AFR) AF: 0.777 AC: 32245 AN: 41484

American (AMR) AF: 0.766 AC: 11697 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2331 AN: 3470

East Asian (EAS) AF: 0.826 AC: 4272 AN: 5172

South Asian (SAS) AF: 0.735 AC: 3542 AN: 4822

European-Finnish (FIN) AF: 0.652 AC: 6898 AN: 10576

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.762 AC: 51818 AN: 67980

Other (OTH) AF: 0.768 AC: 1618 AN: 2108

Alfa AF: 0.759 Hom.: 53175

Bravo AF: 0.771

Asia WGS AF: 0.796 AC: 2771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.5
DANN	Benign	0.52
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3132726;

hg19: chr6-29823606;