rs36038753

Variant names:

• chr17-39879117-G-T
• rs36038753

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 0.389 in 151,738 control chromosomes in the GnomAD database, including 12,233 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 0.39 (12233 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.581

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 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: 0.389 AC: 59022 AN: 151620 Hom.: 12221 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.416

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.389 AC: 59071 AN: 151738 Hom.: 12233 Cov.: 32 AF XY: 0.392 AC XY: 29076 AN XY: 74158

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.416

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.532

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.375

Alfa AF: 0.399 Hom.: 1533

Bravo AF: 0.367

Asia WGS AF: 0.369 AC: 1278 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36038753; hg19: chr17-38035370;