18-3062583-T-C

Variant names:

• chr18-3062583-T-C
• rs9955849

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 0.312 in 152,002 control chromosomes in the GnomAD database, including 8,411 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 0.31 (8411 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.484 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: 0.312 AC: 47372 AN: 151882 Hom.: 8398 Cov.: 32

Gnomad AFR AF: 0.489

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.312 AC: 47418 AN: 152002 Hom.: 8411 Cov.: 32 AF XY: 0.309 AC XY: 22924 AN XY: 74288

Gnomad4 AFR AF: 0.489

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.277

Alfa AF: 0.258 Hom.: 7459

Bravo AF: 0.315

Asia WGS AF: 0.253 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9955849; hg19: chr18-3062581;