chr6-29639269-G-C

Variant names:

• chr6-29639269-G-C
• rs3095267
• ENST00000782059.1:n.436-3079C>G

Variant summary

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

The ENST00000782059.1(ENSG00000301820):​n.436-3079C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.18 in 151,846 control chromosomes in the GnomAD database, including 2,751 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 0.18 (2751 hom., cov: 32)
• Consequence: ENSG00000301820 ENST00000782059.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 17 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.311 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301820	ENST00000782059.1		n.436-3079C>G		intron	N/A
	ENSG00000301820	ENST00000782060.1		n.432-3079C>G		intron	N/A
	ENSG00000301820	ENST00000782061.1		n.312-3079C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27281 AN: 151736 Hom.: 2740 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.180 AC: 27321 AN: 151846 Hom.: 2751 Cov.: 32 AF XY: 0.179 AC XY: 13305 AN XY: 74210

African (AFR) AF: 0.104 AC: 4309 AN: 41434

American (AMR) AF: 0.214 AC: 3257 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.324 AC: 1669 AN: 5148

South Asian (SAS) AF: 0.312 AC: 1497 AN: 4800

European-Finnish (FIN) AF: 0.124 AC: 1308 AN: 10516

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 13983 AN: 67910

Other (OTH) AF: 0.182 AC: 385 AN: 2114

Alfa AF: 0.176 Hom.: 298

Bravo AF: 0.179

Asia WGS AF: 0.388 AC: 1353 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.13
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3095267; hg19: chr6-29607046;