6-134053268-G-C

Variant names:

• chr6-134053268-G-C
• rs1385068
• ENST00000826528.1:n.170+795G>C

Variant summary

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

The ENST00000826528.1(ENSG00000307482):​n.170+795G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.624 in 152,040 control chromosomes in the GnomAD database, including 30,956 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 0.62 (30956 hom., cov: 32)
• Consequence: ENSG00000307482 ENST00000826528.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.936
• Publications: 2 publications found

Genes affected

ENSG00000307482 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.801 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
ENSG00000307482	ENST00000826528.1	n.170+795G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94709 AN: 151922 Hom.: 30911 Cov.: 32

Gnomad AFR AF: 0.809

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.566

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.624 AC: 94811 AN: 152040 Hom.: 30956 Cov.: 32 AF XY: 0.620 AC XY: 46030 AN XY: 74298

African (AFR) AF: 0.809 AC: 33553 AN: 41488

American (AMR) AF: 0.567 AC: 8656 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1893 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1301 AN: 5172

South Asian (SAS) AF: 0.673 AC: 3243 AN: 4818

European-Finnish (FIN) AF: 0.540 AC: 5693 AN: 10534

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.566 AC: 38480 AN: 67970

Other (OTH) AF: 0.606 AC: 1282 AN: 2114

Alfa AF: 0.475 Hom.: 1263

Bravo AF: 0.628

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.32
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs1385068; hg19: chr6-134374406;