chr17-65319878-T-C

Variant names:

• chr17-65319878-T-C
• rs8068707

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 0.267 in 152,094 control chromosomes in the GnomAD database, including 6,249 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 (6249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 3 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 (AMR) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40602 AN: 151976 Hom.: 6232 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.267 AC: 40658 AN: 152094 Hom.: 6249 Cov.: 32 AF XY: 0.268 AC XY: 19947 AN XY: 74348

African (AFR) AF: 0.372 AC: 15406 AN: 41462

American (AMR) AF: 0.405 AC: 6181 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 939 AN: 3470

East Asian (EAS) AF: 0.351 AC: 1811 AN: 5160

South Asian (SAS) AF: 0.206 AC: 994 AN: 4814

European-Finnish (FIN) AF: 0.164 AC: 1738 AN: 10588

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12816 AN: 68000

Other (OTH) AF: 0.246 AC: 520 AN: 2116

Alfa AF: 0.221 Hom.: 18457

Bravo AF: 0.294

Asia WGS AF: 0.284 AC: 987 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	1.4
DANN	Benign	0.40
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs8068707; hg19: chr17-63315996;