chr17-39667885-G-T

Position:

• chr17-39667885-G-T

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 0.032 in 146,222 control chromosomes in the GnomAD database, including 113 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 0.032 (113 hom., cov: 25)
  • Exomes 𝑓: 0.0069 (0 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0503 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: 0.0321 AC: 4682 AN: 145966 Hom.: 113 Cov.: 25

Gnomad AFR AF: 0.0118

Gnomad AMI AF: 0.0459

Gnomad AMR AF: 0.0186

Gnomad ASJ AF: 0.00645

Gnomad EAS AF: 0.000667

Gnomad SAS AF: 0.00379

Gnomad FIN AF: 0.0396

Gnomad MID AF: 0.0128

Gnomad NFE AF: 0.0517

Gnomad OTH AF: 0.0257

GnomAD4 exome AF: 0.00694 AC: 1 AN: 144 Hom.: 0 AF XY: 0.00943 AC XY: 1 AN XY: 106

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.00877

GnomAD4 genome AF: 0.0321 AC: 4684 AN: 146078 Hom.: 113 Cov.: 25 AF XY: 0.0297 AC XY: 2119 AN XY: 71238

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0186

Gnomad4 ASJ AF: 0.00645

Gnomad4 EAS AF: 0.000668

Gnomad4 SAS AF: 0.00378

Gnomad4 FIN AF: 0.0396

Gnomad4 NFE AF: 0.0517

Gnomad4 OTH AF: 0.0254

Alfa AF: 0.0375 Hom.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.3
DANN	Benign	0.91

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2934966; hg19: chr17-37824138;