6-29648045-A-G

Variant names:

• chr6-29648045-A-G
• rs3129073
• ENST00000782059.1:n.435+6351T>C

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.435+6351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,136 control chromosomes in the GnomAD database, including 2,411 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 0.16 (2411 hom., cov: 32)
• Consequence: ENSG00000301820 ENST00000782059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.773
• Publications: 36 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.314 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.435+6351T>C		intron	N/A
	ENSG00000301820	ENST00000782060.1		n.431+6351T>C		intron	N/A
	ENSG00000301820	ENST00000782061.1		n.311+7645T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24664 AN: 152018 Hom.: 2399 Cov.: 32

Gnomad AFR AF: 0.0667

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.162 AC: 24691 AN: 152136 Hom.: 2411 Cov.: 32 AF XY: 0.162 AC XY: 12078 AN XY: 74362

African (AFR) AF: 0.0667 AC: 2770 AN: 41508

American (AMR) AF: 0.177 AC: 2702 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 512 AN: 3466

East Asian (EAS) AF: 0.327 AC: 1692 AN: 5176

South Asian (SAS) AF: 0.309 AC: 1492 AN: 4822

European-Finnish (FIN) AF: 0.124 AC: 1312 AN: 10584

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13579 AN: 67998

Other (OTH) AF: 0.162 AC: 343 AN: 2112

Alfa AF: 0.195 Hom.: 12473

Bravo AF: 0.157

Asia WGS AF: 0.384 AC: 1338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.77

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: rs3129073;

hg19: chr6-29615822;