rs2678787

Variant names:

• chr18-30602362-C-T
• rs2678787

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 0.69 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.664 AC: 27544 AN: 41474

American (AMR) AF: 0.746 AC: 11378 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.519 AC: 2682 AN: 5166

South Asian (SAS) AF: 0.663 AC: 3197 AN: 4822

European-Finnish (FIN) AF: 0.677 AC: 7159 AN: 10582

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48714 AN: 67960

Other (OTH) AF: 0.700 AC: 1476 AN: 2110

Alfa AF: 0.712 Hom.: 37198

Bravo AF: 0.697

Asia WGS AF: 0.615 AC: 2139 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.73
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs2678787; hg19: chr18-28182328;