rs17128007

Variant names:

• chr8-19225642-C-T
• rs17128007
• ENST00000807968.1:n.500G>A

Variant summary

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

The ENST00000807968.1(ENSG00000253557):​n.500G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,210 control chromosomes in the GnomAD database, including 148 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 0.034 (148 hom., cov: 32)
• Consequence: ENSG00000253557 ENST00000807968.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• Publications: 4 publications found

Genes affected

ENSG00000253557 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0734 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807968.1. 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
	LOC100128993	NR_038919.1		n.568+1526G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253557	ENST00000807968.1		n.500G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000253557	ENST00000517949.5	TSL:3	n.535+1526G>A		intron	N/A
	ENSG00000253557	ENST00000518417.1	TSL:4	n.278+1526G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0342 AC: 5198 AN: 152092 Hom.: 148 Cov.: 32

Gnomad AFR AF: 0.0757

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0303

Gnomad FIN AF: 0.0294

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0174

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0342 AC: 5201 AN: 152210 Hom.: 148 Cov.: 32 AF XY: 0.0343 AC XY: 2553 AN XY: 74412

African (AFR) AF: 0.0756 AC: 3139 AN: 41524

American (AMR) AF: 0.0158 AC: 242 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0248 AC: 86 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5160

South Asian (SAS) AF: 0.0300 AC: 144 AN: 4808

European-Finnish (FIN) AF: 0.0294 AC: 312 AN: 10614

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0174 AC: 1184 AN: 68026

Other (OTH) AF: 0.0270 AC: 57 AN: 2112

Alfa AF: 0.0247 Hom.: 34

Bravo AF: 0.0335

Asia WGS AF: 0.0170 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.063
DANN	Benign	0.52
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs17128007; hg19: chr8-19083152;