17-18074612-T-C

Position:

• chr17-18074612-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.4 in 151,898 control chromosomes in the GnomAD database, including 13,040 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 0.40 (13040 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60753 AN: 151780 Hom.: 13021 Cov.: 31

Gnomad AFR AF: 0.430

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.408

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.400 AC: 60808 AN: 151898 Hom.: 13040 Cov.: 31 AF XY: 0.412 AC XY: 30611 AN XY: 74240

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.454

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.758

Gnomad4 SAS AF: 0.707

Gnomad4 FIN AF: 0.408

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.395

Alfa AF: 0.370 Hom.: 2247

Bravo AF: 0.402

Asia WGS AF: 0.679 AC: 2358 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.60
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4426402; hg19: chr17-17977926;