rs2678787

Variant names:

• chr18-30602362-C-T
• rs2678787

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 0.69 in 152,048 control chromosomes in the GnomAD database, including 36,506 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 0.69 (36506 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.636

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.734 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: 0.690 AC: 104894 AN: 151932 Hom.: 36465 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.745

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.663

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.690 AC: 104987 AN: 152048 Hom.: 36506 Cov.: 32 AF XY: 0.686 AC XY: 50955 AN XY: 74296

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.746

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.519

Gnomad4 SAS AF: 0.663

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.700

Alfa AF: 0.711 Hom.: 30316

Bravo AF: 0.697

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2678787; hg19: chr18-28182328;