8-59266527-G-T

Variant names:

• chr8-59266527-G-T
• rs7837791
• ENST00000794042.1:n.183+3395G>T

Variant summary

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

The ENST00000794042.1(ENSG00000303378):​n.183+3395G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,392 control chromosomes in the GnomAD database, including 22,136 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 0.53 (22136 hom., cov: 31)
• Consequence: ENSG00000303378 ENST00000794042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 20 publications found

Genes affected

ENSG00000303378 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794042.1. 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
	ENSG00000303378	ENST00000794042.1		n.183+3395G>T		intron	N/A
	ENSG00000303378	ENST00000794043.1		n.280+3395G>T		intron	N/A
	ENSG00000303378	ENST00000794044.1		n.298+3395G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80476 AN: 151284 Hom.: 22099 Cov.: 31

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.451

Gnomad EAS AF: 0.493

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.532 AC: 80569 AN: 151392 Hom.: 22136 Cov.: 31 AF XY: 0.527 AC XY: 38960 AN XY: 73900

African (AFR) AF: 0.638 AC: 26373 AN: 41352

American (AMR) AF: 0.625 AC: 9515 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.451 AC: 1564 AN: 3470

East Asian (EAS) AF: 0.494 AC: 2548 AN: 5162

South Asian (SAS) AF: 0.288 AC: 1372 AN: 4770

European-Finnish (FIN) AF: 0.456 AC: 4666 AN: 10238

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.480 AC: 32604 AN: 67868

Other (OTH) AF: 0.548 AC: 1153 AN: 2104

Alfa AF: 0.500 Hom.: 76955

Bravo AF: 0.560

Asia WGS AF: 0.398 AC: 1383 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.1
DANN	Benign	0.58
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs7837791; hg19: chr8-60179086;