6-50868566-G-A

Variant names:

• chr6-50868566-G-A
• rs734597
• ENST00000791176.1:n.342-6110G>A

Variant summary

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

The ENST00000791176.1(ENSG00000303025):​n.342-6110G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.163 in 152,018 control chromosomes in the GnomAD database, including 2,286 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 (2286 hom., cov: 32)
• Consequence: ENSG00000303025 ENST00000791176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 31 publications found

Genes affected

ENSG00000303025 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000791176.1. 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
	ENSG00000303025	ENST00000791176.1		n.342-6110G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.163 AC: 24785 AN: 151900 Hom.: 2287 Cov.: 32

Gnomad AFR AF: 0.0938

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.269

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.163 AC: 24790 AN: 152018 Hom.: 2286 Cov.: 32 AF XY: 0.165 AC XY: 12286 AN XY: 74274

African (AFR) AF: 0.0936 AC: 3886 AN: 41504

American (AMR) AF: 0.269 AC: 4098 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 513 AN: 3470

East Asian (EAS) AF: 0.168 AC: 862 AN: 5140

South Asian (SAS) AF: 0.229 AC: 1105 AN: 4822

European-Finnish (FIN) AF: 0.184 AC: 1944 AN: 10564

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11897 AN: 67962

Other (OTH) AF: 0.165 AC: 347 AN: 2104

Alfa AF: 0.170 Hom.: 6289

Bravo AF: 0.167

Asia WGS AF: 0.227 AC: 789 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.35
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs734597; hg19: chr6-50836279;