18-75795614-T-G

Variant names:

• chr18-75795614-T-G
• rs12326088

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 0.556 in 152,060 control chromosomes in the GnomAD database, including 26,807 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 0.56 (26807 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.418
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.557 AC: 84565 AN: 151940 Hom.: 26815 Cov.: 32

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.688

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.556 AC: 84563 AN: 152060 Hom.: 26807 Cov.: 32 AF XY: 0.559 AC XY: 41560 AN XY: 74324

African (AFR) AF: 0.230 AC: 9540 AN: 41484

American (AMR) AF: 0.566 AC: 8647 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1902 AN: 3470

East Asian (EAS) AF: 0.709 AC: 3655 AN: 5156

South Asian (SAS) AF: 0.708 AC: 3412 AN: 4816

European-Finnish (FIN) AF: 0.686 AC: 7250 AN: 10576

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48110 AN: 67960

Other (OTH) AF: 0.574 AC: 1213 AN: 2112

Alfa AF: 0.628 Hom.: 66172

Bravo AF: 0.529

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.74
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs12326088; hg19: chr18-73507569;