8-6926753-C-T

Variant names:

• chr8-6926753-C-T
• rs3824304
• ENST00000734108.1:n.367-43C>T

Variant summary

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

The ENST00000734108.1(ENSG00000295932):​n.367-43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,224 control chromosomes in the GnomAD database, including 555 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 0.072 (555 hom., cov: 33)
• Consequence: ENSG00000295932 ENST00000734108.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.213 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.367-43C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0717 AC: 10899 AN: 152106 Hom.: 555 Cov.: 33

Gnomad AFR AF: 0.0285

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.224

Gnomad SAS AF: 0.0871

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0627

Gnomad OTH AF: 0.0649

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

GnomAD4 genome AF: 0.0716 AC: 10905 AN: 152224 Hom.: 555 Cov.: 33 AF XY: 0.0782 AC XY: 5821 AN XY: 74426

African (AFR) AF: 0.0286 AC: 1186 AN: 41540

American (AMR) AF: 0.138 AC: 2113 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0874 AC: 303 AN: 3466

East Asian (EAS) AF: 0.224 AC: 1159 AN: 5176

South Asian (SAS) AF: 0.0869 AC: 419 AN: 4820

European-Finnish (FIN) AF: 0.116 AC: 1232 AN: 10586

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0627 AC: 4264 AN: 68018

Other (OTH) AF: 0.0633 AC: 134 AN: 2116

Alfa AF: 0.0699 Hom.: 88

Bravo AF: 0.0712

Asia WGS AF: 0.153 AC: 531 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.36
DANN	Benign	0.37
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs3824304; hg19: chr8-6784275;