rs73317122

Positions:

• chr17-26993863-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

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 0.44 (0 hom., cov: 36)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.44

Genes affected

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.26993863G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000264734	ENST00000580686.1	n.118-2250C>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 34377 AN: 77722 Hom.: 0 Cov.: 36 FAILED QC

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.434

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: InbreedingCoeff AF: 0.442 AC: 34398 AN: 77776 Hom.: 0 Cov.: 36 AF XY: 0.441 AC XY: 17071 AN XY: 38744

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.457

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.433

Alfa AF: 0.464 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.91
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73317122; hg19: chr17-25320889; COSMIC: COSV73869410;