17-39583908-T-C

Variant names:

• chr17-39583908-T-C
• rs1877030

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 0.816 in 152,110 control chromosomes in the GnomAD database, including 50,856 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 0.82 (50856 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 37 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.906 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: 0.816 AC: 123993 AN: 151992 Hom.: 50802 Cov.: 30

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.929

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.816 AC: 124112 AN: 152110 Hom.: 50856 Cov.: 30 AF XY: 0.818 AC XY: 60865 AN XY: 74362

African (AFR) AF: 0.775 AC: 32113 AN: 41456

American (AMR) AF: 0.758 AC: 11584 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2661 AN: 3470

East Asian (EAS) AF: 0.758 AC: 3924 AN: 5176

South Asian (SAS) AF: 0.928 AC: 4478 AN: 4824

European-Finnish (FIN) AF: 0.918 AC: 9735 AN: 10602

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56953 AN: 67986

Other (OTH) AF: 0.812 AC: 1719 AN: 2116

Alfa AF: 0.828 Hom.: 97700

Bravo AF: 0.798

Asia WGS AF: 0.865 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1877030; hg19: chr17-37740161;