rs17083037

Positions:

• chr18-70713005-T-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;