17-68784254-T-C

Variant names:

• chr17-68784254-T-C
• rs755424

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 0.275 in 152,196 control chromosomes in the GnomAD database, including 6,021 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 0.27 (6021 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.468 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41738 AN: 152078 Hom.: 6001 Cov.: 33

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.275 AC: 41784 AN: 152196 Hom.: 6021 Cov.: 33 AF XY: 0.279 AC XY: 20775 AN XY: 74386

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.484

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.276

Alfa AF: 0.271 Hom.: 9166

Bravo AF: 0.283

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs755424; hg19: chr17-66780395;