18-51256972-T-C

Variant names:

• chr18-51256972-T-C
• rs10853605

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 0.432 in 151,972 control chromosomes in the GnomAD database, including 14,660 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 0.43 (14660 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.968
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.432 AC: 65543 AN: 151854 Hom.: 14647 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.508

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.449

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

GnomAD4 genome AF: 0.432 AC: 65576 AN: 151972 Hom.: 14660 Cov.: 32 AF XY: 0.439 AC XY: 32626 AN XY: 74278

African (AFR) AF: 0.333 AC: 13788 AN: 41444

American (AMR) AF: 0.506 AC: 7724 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1467 AN: 3470

East Asian (EAS) AF: 0.581 AC: 3006 AN: 5178

South Asian (SAS) AF: 0.526 AC: 2535 AN: 4816

European-Finnish (FIN) AF: 0.498 AC: 5254 AN: 10542

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.445 AC: 30228 AN: 67956

Other (OTH) AF: 0.450 AC: 950 AN: 2110

Alfa AF: 0.447 Hom.: 65276

Bravo AF: 0.433

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	0.79
DANN	Benign	0.69
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs10853605; hg19: chr18-48783342;