18-51878594-T-G

Variant names:

• chr18-51878594-T-G
• rs1351435

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 0.981 in 152,268 control chromosomes in the GnomAD database, including 73,248 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 0.98 (73248 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.988 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: 0.981 AC: 149229 AN: 152150 Hom.: 73208 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.992

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 0.920

Gnomad SAS AF: 0.987

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.994

Gnomad OTH AF: 0.986

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

GnomAD4 genome AF: 0.981 AC: 149327 AN: 152268 Hom.: 73248 Cov.: 32 AF XY: 0.980 AC XY: 72946 AN XY: 74452

African (AFR) AF: 0.961 AC: 39934 AN: 41572

American (AMR) AF: 0.992 AC: 15171 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3449 AN: 3470

East Asian (EAS) AF: 0.920 AC: 4753 AN: 5168

South Asian (SAS) AF: 0.986 AC: 4764 AN: 4830

European-Finnish (FIN) AF: 0.978 AC: 10382 AN: 10618

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.994 AC: 67589 AN: 67996

Other (OTH) AF: 0.986 AC: 2081 AN: 2110

Alfa AF: 0.987 Hom.: 102442

Bravo AF: 0.981

Asia WGS AF: 0.952 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.56
DANN	Benign	0.54
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1351435; hg19: chr18-49404964;