8-1730091-G-T

Variant names:

• chr8-1730091-G-T
• rs12545625
• ENST00000517626.1:n.-115G>T

Variant summary

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

The ENST00000517626.1(ENSG00000254265):​n.-115G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,092 control chromosomes in the GnomAD database, including 4,463 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 0.24 (4463 hom., cov: 33)
  • Exomes 𝑓: 0.18 (0 hom.)
• Consequence: ENSG00000254265 ENST00000517626.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 0 publications found

Genes affected

ENSG00000254265 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517626.1. 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
	ENSG00000254265	ENST00000517626.1	TSL:6	n.-115G>T		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35888 AN: 151936 Hom.: 4462 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.112

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.258

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.184 AC: 7 AN: 38 Hom.: 0 AF XY: 0.167 AC XY: 5 AN XY: 30

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.115 AC: 3 AN: 26

Other (OTH) AF: 0.500 AC: 2 AN: 4

GnomAD4 genome AF: 0.236 AC: 35914 AN: 152054 Hom.: 4463 Cov.: 33 AF XY: 0.237 AC XY: 17640 AN XY: 74336

African (AFR) AF: 0.194 AC: 8026 AN: 41476

American (AMR) AF: 0.261 AC: 3991 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 622 AN: 3470

East Asian (EAS) AF: 0.112 AC: 578 AN: 5172

South Asian (SAS) AF: 0.168 AC: 809 AN: 4818

European-Finnish (FIN) AF: 0.307 AC: 3242 AN: 10570

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

European-Non Finnish (NFE) AF: 0.263 AC: 17853 AN: 67968

Other (OTH) AF: 0.228 AC: 482 AN: 2110

Alfa AF: 0.248 Hom.: 2615

Bravo AF: 0.228

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.24
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs12545625; hg19: chr8-1678257;