rs2887004

Variant names:

• chr18-71712154-A-G
• rs2887004

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 0.12 in 152,042 control chromosomes in the GnomAD database, including 1,513 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 0.12 (1513 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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: 0.120 AC: 18240 AN: 151926 Hom.: 1512 Cov.: 32

Gnomad AFR AF: 0.0322

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00540

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.120 AC: 18250 AN: 152042 Hom.: 1513 Cov.: 32 AF XY: 0.123 AC XY: 9153 AN XY: 74342

Gnomad4 AFR AF: 0.0322

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00541

Gnomad4 SAS AF: 0.104

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.108

Alfa AF: 0.145 Hom.: 341

Bravo AF: 0.109

Asia WGS AF: 0.0540 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.29
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2887004; hg19: chr18-69379390;