rs1667952

Variant names:

• chr18-77146018-A-G
• rs1667952

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.399

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.307

Alfa AF: 0.241 Hom.: 2381

Bravo AF: 0.321

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	5.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1667952; hg19: chr18-74857974;