chr17-20720675-G-T

Variant names:

• chr17-20720675-G-T
• rs10512425
• ENST00000441215.2:n.203+90G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000441215.2(ENSG00000226521):​n.203+90G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000226521 ENST00000441215.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.697
• Publications: 0 publications found

Genes affected

ENSG00000226521 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100287072	NR_172472.1	n.1262+90G>T		intron_variant	Intron 5 of 13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226521	ENST00000441215.2	n.203+90G>T		intron_variant	Intron 2 of 10	6
ENSG00000290430	ENST00000578210.5	n.205+90G>T		intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 439916 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 243456

African (AFR) AF: 0.00 AC: 0 AN: 11938

American (AMR) AF: 0.00 AC: 0 AN: 31544

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12798

East Asian (EAS) AF: 0.00 AC: 0 AN: 24732

South Asian (SAS) AF: 0.00 AC: 0 AN: 59060

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 37006

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2302

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 239052

Other (OTH) AF: 0.00 AC: 0 AN: 21484

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.51
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs10512425; hg19: chr17-20623988;