chr17-39887396-C-T

Variant names:

• chr17-39887396-C-T
• rs12936409

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 0.356 in 151,668 control chromosomes in the GnomAD database, including 11,129 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 0.36 (11129 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.210
• Publications: 31 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.447 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: 0.356 AC: 53888 AN: 151548 Hom.: 11120 Cov.: 29

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.451

Gnomad OTH AF: 0.357

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

GnomAD4 genome AF: 0.356 AC: 53919 AN: 151668 Hom.: 11129 Cov.: 29 AF XY: 0.359 AC XY: 26601 AN XY: 74076

African (AFR) AF: 0.143 AC: 5938 AN: 41412

American (AMR) AF: 0.378 AC: 5756 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1442 AN: 3460

East Asian (EAS) AF: 0.270 AC: 1392 AN: 5158

South Asian (SAS) AF: 0.370 AC: 1780 AN: 4808

European-Finnish (FIN) AF: 0.532 AC: 5543 AN: 10422

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.451 AC: 30620 AN: 67860

Other (OTH) AF: 0.354 AC: 743 AN: 2100

Alfa AF: 0.397 Hom.: 4902

Bravo AF: 0.328

Asia WGS AF: 0.354 AC: 1229 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	6.0
DANN	Benign	0.29
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs12936409; hg19: chr17-38043649;