8-34139533-C-G

Variant names:

• chr8-34139533-C-G
• rs2729993
• ENST00000518217.2:n.172+5774C>G

Variant summary

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

The ENST00000518217.2(ENSG00000254302):​n.172+5774C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 151,872 control chromosomes in the GnomAD database, including 42,291 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 0.74 (42291 hom., cov: 31)
• Consequence: ENSG00000254302 ENST00000518217.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 4 publications found

Genes affected

ENSG00000254302 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.876 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518217.2. 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
	LOC105379364	NR_189605.1		n.955+5774C>G		intron	N/A
	LOC105379364	NR_189606.1		n.431-33444C>G		intron	N/A
	LOC105379364	NR_189607.1		n.501+5774C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254302	ENST00000518217.2	TSL:3	n.172+5774C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.736 AC: 111721 AN: 151754 Hom.: 42237 Cov.: 31

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.716

Gnomad ASJ AF: 0.733

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.673

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.736 AC: 111835 AN: 151872 Hom.: 42291 Cov.: 31 AF XY: 0.728 AC XY: 53999 AN XY: 74202

African (AFR) AF: 0.884 AC: 36646 AN: 41464

American (AMR) AF: 0.716 AC: 10898 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.733 AC: 2541 AN: 3466

East Asian (EAS) AF: 0.373 AC: 1917 AN: 5138

South Asian (SAS) AF: 0.499 AC: 2398 AN: 4810

European-Finnish (FIN) AF: 0.673 AC: 7100 AN: 10552

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.707 AC: 48026 AN: 67904

Other (OTH) AF: 0.748 AC: 1577 AN: 2108

Alfa AF: 0.617 Hom.: 1702

Bravo AF: 0.748

Asia WGS AF: 0.467 AC: 1628 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.26
DANN	Benign	0.41
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2729993; hg19: chr8-33997051;