18-50966123-G-A

Variant names:

• chr18-50966123-G-A
• rs674965

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 0.482 in 151,936 control chromosomes in the GnomAD database, including 18,619 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 0.48 (18619 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.298
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73098 AN: 151818 Hom.: 18584 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.436

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.550

Gnomad SAS AF: 0.324

Gnomad FIN AF: 0.418

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.480

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

GnomAD4 genome AF: 0.482 AC: 73194 AN: 151936 Hom.: 18619 Cov.: 31 AF XY: 0.480 AC XY: 35636 AN XY: 74266

African (AFR) AF: 0.658 AC: 27242 AN: 41400

American (AMR) AF: 0.436 AC: 6661 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1610 AN: 3466

East Asian (EAS) AF: 0.549 AC: 2836 AN: 5162

South Asian (SAS) AF: 0.324 AC: 1560 AN: 4816

European-Finnish (FIN) AF: 0.418 AC: 4415 AN: 10558

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27138 AN: 67952

Other (OTH) AF: 0.483 AC: 1020 AN: 2112

Alfa AF: 0.423 Hom.: 11296

Bravo AF: 0.499

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.15
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs674965; hg19: chr18-48492493;