18-75824756-G-T

Variant names:

• chr18-75824756-G-T
• rs9956878

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 0.49 in 152,098 control chromosomes in the GnomAD database, including 18,708 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 0.49 (18708 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0190
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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: 0.490 AC: 74410 AN: 151980 Hom.: 18668 Cov.: 33

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.470

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

GnomAD4 genome AF: 0.490 AC: 74497 AN: 152098 Hom.: 18708 Cov.: 33 AF XY: 0.485 AC XY: 36035 AN XY: 74342

African (AFR) AF: 0.588 AC: 24406 AN: 41480

American (AMR) AF: 0.460 AC: 7027 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3470

East Asian (EAS) AF: 0.265 AC: 1367 AN: 5166

South Asian (SAS) AF: 0.396 AC: 1911 AN: 4822

European-Finnish (FIN) AF: 0.434 AC: 4588 AN: 10564

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31927 AN: 67996

Other (OTH) AF: 0.463 AC: 975 AN: 2108

Alfa AF: 0.469 Hom.: 74246

Bravo AF: 0.496

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	14
DANN	Benign	0.85
PhyloP100		-0.019

Splicing

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

Other links and lift over

dbSNP: rs9956878; hg19: chr18-73536711;