rs1878680

Variant names:

• chr18-43145430-A-G
• rs1878680

Your query was ambiguous. Multiple possible variants found:

• chr18-43145430-A-G
• chr18-43145430-A-T

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 0.44 in 152,000 control chromosomes in the GnomAD database, including 15,240 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 0.44 (15240 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.543 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: 0.440 AC: 66864 AN: 151882 Hom.: 15213 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.307

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.440 AC: 66946 AN: 152000 Hom.: 15240 Cov.: 32 AF XY: 0.440 AC XY: 32707 AN XY: 74292

Gnomad4 AFR AF: 0.549

Gnomad4 AMR AF: 0.478

Gnomad4 ASJ AF: 0.307

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.390

Alfa AF: 0.378 Hom.: 22611

Bravo AF: 0.453

Asia WGS AF: 0.411 AC: 1428 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.87
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1878680; hg19: chr18-40725395;