17-39892980-T-C

Position:

• chr17-39892980-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 0.451 in 151,984 control chromosomes in the GnomAD database, including 15,768 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 0.45 (15768 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.489 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: 0.451 AC: 68483 AN: 151866 Hom.: 15749 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.493

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.451 AC: 68550 AN: 151984 Hom.: 15768 Cov.: 31 AF XY: 0.452 AC XY: 33575 AN XY: 74274

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.435

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.493

Gnomad4 OTH AF: 0.433

Alfa AF: 0.481 Hom.: 30023

Bravo AF: 0.430

Asia WGS AF: 0.396 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12950743; hg19: chr17-38049233;