chr17-39893336-C-T

Variant names:

• chr17-39893336-C-T
• rs7359623

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 0.441 in 152,022 control chromosomes in the GnomAD database, including 15,199 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 0.44 (15199 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.388

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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: 0.441 AC: 66991 AN: 151904 Hom.: 15180 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.669

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.490

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.441 AC: 67059 AN: 152022 Hom.: 15199 Cov.: 32 AF XY: 0.443 AC XY: 32891 AN XY: 74290

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.434

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.490

Gnomad4 OTH AF: 0.425

Alfa AF: 0.437 Hom.: 2931

Bravo AF: 0.419

Asia WGS AF: 0.394 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.8
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7359623; hg19: chr17-38049589;