chr18-3062583-T-C

Variant names:

• chr18-3062583-T-C
• rs9955849

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 0.312 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.489 AC: 20263 AN: 41414

American (AMR) AF: 0.204 AC: 3123 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1386 AN: 5180

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2830 AN: 10542

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16874 AN: 67984

Other (OTH) AF: 0.277 AC: 583 AN: 2108

Alfa AF: 0.269 Hom.: 19233

Bravo AF: 0.315

Asia WGS AF: 0.253 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.29
DANN	Benign	0.55
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs9955849; hg19: chr18-3062581;