chr17-68784254-T-C

Variant names:

• chr17-68784254-T-C
• rs755424

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.246 AC: 10221 AN: 41518

American (AMR) AF: 0.359 AC: 5494 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.244 AC: 846 AN: 3468

East Asian (EAS) AF: 0.484 AC: 2496 AN: 5158

South Asian (SAS) AF: 0.464 AC: 2233 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2138 AN: 10614

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17440 AN: 68008

Other (OTH) AF: 0.276 AC: 583 AN: 2112

Alfa AF: 0.272 Hom.: 14014

Bravo AF: 0.283

Asia WGS AF: 0.491 AC: 1705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs755424; hg19: chr17-66780395;