rs1667952

Variant names:

• chr18-77146018-A-G
• rs1667952

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 0.308 in 152,122 control chromosomes in the GnomAD database, including 8,626 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 (8626 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.511 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: 0.308 AC: 46820 AN: 152004 Hom.: 8624 Cov.: 33

Gnomad AFR AF: 0.517

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.308 AC: 46855 AN: 152122 Hom.: 8626 Cov.: 33 AF XY: 0.308 AC XY: 22931 AN XY: 74376

African (AFR) AF: 0.517 AC: 21421 AN: 41464

American (AMR) AF: 0.262 AC: 4004 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1202 AN: 3472

East Asian (EAS) AF: 0.266 AC: 1378 AN: 5182

South Asian (SAS) AF: 0.399 AC: 1926 AN: 4824

European-Finnish (FIN) AF: 0.221 AC: 2341 AN: 10572

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.201 AC: 13647 AN: 68000

Other (OTH) AF: 0.307 AC: 648 AN: 2110

Alfa AF: 0.239 Hom.: 2576

Bravo AF: 0.321

Asia WGS AF: 0.379 AC: 1320 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	5.2
DANN	Benign	0.72
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1667952; hg19: chr18-74857974;