chr8-8739561-G-A

Variant names:

• chr8-8739561-G-A
• rs6601729
• ENST00000522213.5:n.624+14439C>T

Variant summary

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

The ENST00000522213.5(ENSG00000254367):​n.624+14439C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,792 control chromosomes in the GnomAD database, including 6,164 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 0.26 (6164 hom., cov: 30)
• Consequence: ENSG00000254367 ENST00000522213.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640
• Publications: 4 publications found

Genes affected

ENSG00000254367 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254367	ENST00000522213.5	n.624+14439C>T		intron_variant	Intron 3 of 3	2
ENSG00000254367	ENST00000765578.1	n.456-15827C>T		intron_variant	Intron 2 of 3
ENSG00000254367	ENST00000765579.1	n.407-14522C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40072 AN: 151674 Hom.: 6148 Cov.: 30

Gnomad AFR AF: 0.402

Gnomad AMI AF: 0.246

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.264 AC: 40121 AN: 151792 Hom.: 6164 Cov.: 30 AF XY: 0.255 AC XY: 18881 AN XY: 74188

African (AFR) AF: 0.402 AC: 16630 AN: 41350

American (AMR) AF: 0.187 AC: 2859 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3468

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.136 AC: 653 AN: 4798

European-Finnish (FIN) AF: 0.152 AC: 1591 AN: 10488

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.243 AC: 16503 AN: 67922

Other (OTH) AF: 0.254 AC: 534 AN: 2104

Alfa AF: 0.264 Hom.: 2438

Bravo AF: 0.272

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.3
DANN	Benign	0.49
PhyloP100		0.064

Splicing

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

Other links and lift over

dbSNP: rs6601729; hg19: chr8-8597071;