rs17083037

Variant names:

• chr18-70713005-T-G
• rs17083037

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 0.0573 in 152,264 control chromosomes in the GnomAD database, including 280 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 0.057 (280 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.264

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0815 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: 0.0572 AC: 8705 AN: 152146 Hom.: 276 Cov.: 32

Gnomad AFR AF: 0.0833

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0439

Gnomad ASJ AF: 0.0412

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0605

Gnomad FIN AF: 0.0473

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0499

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0573 AC: 8732 AN: 152264 Hom.: 280 Cov.: 32 AF XY: 0.0562 AC XY: 4186 AN XY: 74448

Gnomad4 AFR AF: 0.0838

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.0412

Gnomad4 EAS AF: 0.00561

Gnomad4 SAS AF: 0.0608

Gnomad4 FIN AF: 0.0473

Gnomad4 NFE AF: 0.0499

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0511 Hom.: 189

Bravo AF: 0.0579

Asia WGS AF: 0.0450 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17083037; hg19: chr18-68380241;