8-6926734-C-T

Variant names:

• chr8-6926734-C-T
• rs2741689
• ENST00000734108.1:n.367-62C>T

Variant summary

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

The ENST00000734108.1(ENSG00000295932):​n.367-62C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 152,196 control chromosomes in the GnomAD database, including 50,106 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 0.81 (50106 hom., cov: 33)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.481
• Publications: 4 publications found

Genes affected

ENSG00000295932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000734108.1. 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
	ENSG00000295932	ENST00000734108.1		n.367-62C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.811 AC: 123289 AN: 152078 Hom.: 50085 Cov.: 33

Gnomad AFR AF: 0.816

Gnomad AMI AF: 0.830

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.844

Gnomad SAS AF: 0.785

Gnomad FIN AF: 0.749

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.811 AC: 123367 AN: 152196 Hom.: 50106 Cov.: 33 AF XY: 0.808 AC XY: 60139 AN XY: 74402

African (AFR) AF: 0.816 AC: 33891 AN: 41536

American (AMR) AF: 0.798 AC: 12206 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.881 AC: 3059 AN: 3472

East Asian (EAS) AF: 0.843 AC: 4370 AN: 5182

South Asian (SAS) AF: 0.785 AC: 3784 AN: 4820

European-Finnish (FIN) AF: 0.749 AC: 7923 AN: 10578

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55376 AN: 67990

Other (OTH) AF: 0.822 AC: 1738 AN: 2114

Alfa AF: 0.815 Hom.: 108365

Bravo AF: 0.814

Asia WGS AF: 0.835 AC: 2906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.45
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs2741689; hg19: chr8-6784256;