chr17-31006498-T-C

Variant names:

• chr17-31006498-T-C
• rs17826255
• ENST00000754467.1:n.493-18462A>G

Variant summary

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

The ENST00000754467.1(ENSG00000298294):​n.493-18462A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0469 in 152,288 control chromosomes in the GnomAD database, including 319 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 0.047 (319 hom., cov: 30)
• Consequence: ENSG00000298294 ENST00000754467.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.437
• Publications: 13 publications found

Genes affected

ENSG00000298294 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000754467.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000298294	ENST00000754467.1		n.493-18462A>G		intron	N/A
	ENSG00000298294	ENST00000754468.1		n.528-18462A>G		intron	N/A
	ENSG00000298294	ENST00000754469.1		n.463-18462A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7135 AN: 152170 Hom.: 316 Cov.: 30

Gnomad AFR AF: 0.0128

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.0622

Gnomad ASJ AF: 0.0703

Gnomad EAS AF: 0.199

Gnomad SAS AF: 0.0379

Gnomad FIN AF: 0.0236

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0542

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0469 AC: 7143 AN: 152288 Hom.: 319 Cov.: 30 AF XY: 0.0455 AC XY: 3388 AN XY: 74462

African (AFR) AF: 0.0127 AC: 530 AN: 41578

American (AMR) AF: 0.0620 AC: 949 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0703 AC: 244 AN: 3472

East Asian (EAS) AF: 0.199 AC: 1032 AN: 5176

South Asian (SAS) AF: 0.0381 AC: 184 AN: 4828

European-Finnish (FIN) AF: 0.0236 AC: 250 AN: 10604

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0543 AC: 3690 AN: 68006

Other (OTH) AF: 0.0676 AC: 143 AN: 2116

Alfa AF: 0.0538 Hom.: 1078

Bravo AF: 0.0504

Asia WGS AF: 0.117 AC: 404 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.2
DANN	Benign	0.097
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs17826255; hg19: chr17-29333516;