17-30237328-T-G

Variant names:

• chr17-30237328-T-G
• rs25531
• ENST00000724731.1:n.109+258T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000724731.1(ENSG00000266120):​n.109+258T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 4)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000266120 ENST00000724731.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.732
• Publications: 749 publications found

Genes affected

ENSG00000266120 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105371720	XR_001752824.2	n.280+258T>G		intron_variant	Intron 1 of 3
LOC105371720	XR_007065695.1	n.-170T>G		upstream_gene_variant
LOC105371720	XR_007065696.1	n.-170T>G		upstream_gene_variant
LOC105371720	XR_007065698.1	n.-170T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000266120	ENST00000724731.1	n.109+258T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 31512 Hom.: 0 Cov.: 4

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 31512 Hom.: 0 Cov.: 4 AF XY: 0.00 AC XY: 0 AN XY: 14006

African (AFR) AF: 0.00 AC: 0 AN: 9032

American (AMR) AF: 0.00 AC: 0 AN: 1922

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 844

East Asian (EAS) AF: 0.00 AC: 0 AN: 608

South Asian (SAS) AF: 0.00 AC: 0 AN: 546

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 1128

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 32

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 16790

Other (OTH) AF: 0.00 AC: 0 AN: 402

Alfa AF: 0.00 Hom.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.2
DANN	Benign	0.39
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs25531; hg19: chr17-28564346;