18-47177413-T-G

Variant names:

• chr18-47177413-T-G
• rs2932126

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 0.426 in 151,628 control chromosomes in the GnomAD database, including 14,037 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 0.43 (14037 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.265
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 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: 0.426 AC: 64568 AN: 151510 Hom.: 14036 Cov.: 31

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.394

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.426 AC: 64583 AN: 151628 Hom.: 14037 Cov.: 31 AF XY: 0.425 AC XY: 31456 AN XY: 74096

African (AFR) AF: 0.344 AC: 14219 AN: 41308

American (AMR) AF: 0.438 AC: 6676 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1821 AN: 3466

East Asian (EAS) AF: 0.210 AC: 1081 AN: 5156

South Asian (SAS) AF: 0.393 AC: 1883 AN: 4792

European-Finnish (FIN) AF: 0.507 AC: 5322 AN: 10492

Middle Eastern (MID) AF: 0.554 AC: 163 AN: 294

European-Non Finnish (NFE) AF: 0.470 AC: 31918 AN: 67854

Other (OTH) AF: 0.428 AC: 898 AN: 2100

Alfa AF: 0.433 Hom.: 5661

Bravo AF: 0.419

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.7
DANN	Benign	0.40
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2932126; hg19: chr18-44703784;