chr8-27594724-G-GT

Variant names:

• chr8-27594724-G-GT
• rs35598594
• ENST00000774578.1:n.169+2113dupT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000774578.1(ENSG00000300853):​n.169+2113dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,188 control chromosomes in the GnomAD database, including 1,163 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1163 hom., cov: 30)
• Consequence: ENSG00000300853 ENST00000774578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.478
• Publications: 1 publications found

Genes affected

ENSG00000300853 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000774578.1. 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
	ENSG00000300853	ENST00000774578.1		n.169+2113dupT		intron	N/A
	ENSG00000300853	ENST00000774579.1		n.284+1426dupT		intron	N/A
	ENSG00000300853	ENST00000774580.1		n.128+1467dupT		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16279 AN: 152070 Hom.: 1163 Cov.: 30

Gnomad AFR AF: 0.0279

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0920

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.107 AC: 16285 AN: 152188 Hom.: 1163 Cov.: 30 AF XY: 0.104 AC XY: 7727 AN XY: 74392

African (AFR) AF: 0.0278 AC: 1157 AN: 41550

American (AMR) AF: 0.100 AC: 1533 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 615 AN: 3468

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0929 AC: 448 AN: 4820

European-Finnish (FIN) AF: 0.123 AC: 1300 AN: 10576

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10860 AN: 67986

Other (OTH) AF: 0.120 AC: 253 AN: 2108

Alfa AF: 0.132 Hom.: 189

Bravo AF: 0.101

Asia WGS AF: 0.0370 AC: 128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs35598594; hg19: chr8-27452241;