rs2115980

Variant names:

• chr18-73888141-C-A
• rs2115980

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 0.449 in 151,980 control chromosomes in the GnomAD database, including 16,949 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 0.45 (16949 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.532 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: 0.449 AC: 68196 AN: 151862 Hom.: 16940 Cov.: 32

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.524

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.546

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.449 AC: 68233 AN: 151980 Hom.: 16949 Cov.: 32 AF XY: 0.454 AC XY: 33746 AN XY: 74270

African (AFR) AF: 0.215 AC: 8909 AN: 41490

American (AMR) AF: 0.525 AC: 8013 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2220 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2680 AN: 5146

South Asian (SAS) AF: 0.548 AC: 2635 AN: 4810

European-Finnish (FIN) AF: 0.546 AC: 5758 AN: 10542

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.536 AC: 36438 AN: 67936

Other (OTH) AF: 0.485 AC: 1025 AN: 2112

Alfa AF: 0.515 Hom.: 88172

Bravo AF: 0.435

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.30
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs2115980; hg19: chr18-71555376;