6-58409602-T-G

Variant names:

• chr6-58409602-T-G
• rs2343013
• ENST00000641775.1:n.457-26957T>G

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.457-26957T>G variant causes a intron change. The variant allele was found at a frequency of 0.792 in 151,824 control chromosomes in the GnomAD database, including 47,770 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 0.79 (47770 hom., cov: 32)
• Consequence: ENSG00000225096 ENST00000641775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641775.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000225096	ENST00000641775.1		n.457-26957T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.792 AC: 120157 AN: 151704 Hom.: 47744 Cov.: 32

Gnomad AFR AF: 0.736

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.842

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.798

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

GnomAD4 genome AF: 0.792 AC: 120229 AN: 151824 Hom.: 47770 Cov.: 32 AF XY: 0.791 AC XY: 58643 AN XY: 74154

African (AFR) AF: 0.736 AC: 30509 AN: 41458

American (AMR) AF: 0.835 AC: 12702 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.814 AC: 2822 AN: 3468

East Asian (EAS) AF: 0.731 AC: 3736 AN: 5114

South Asian (SAS) AF: 0.748 AC: 3609 AN: 4826

European-Finnish (FIN) AF: 0.842 AC: 8892 AN: 10562

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55343 AN: 67878

Other (OTH) AF: 0.793 AC: 1670 AN: 2106

Alfa AF: 0.796 Hom.: 12573

Bravo AF: 0.789

Asia WGS AF: 0.673 AC: 2339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.22

Splicing

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

Other links and lift over

dbSNP: rs2343013; hg19: chr6-58735880;