chr18-61226757-C-T

Variant names:

• chr18-61226757-C-T
• rs10503051

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 0.00878 in 152,084 control chromosomes in the GnomAD database, including 19 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 0.0088 (19 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.06
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0588 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.00883 AC: 1342 AN: 151966 Hom.: 19 Cov.: 32

Gnomad AFR AF: 0.00229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0183

Gnomad ASJ AF: 0.00347

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.0209

Gnomad FIN AF: 0.00368

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00686

Gnomad OTH AF: 0.00766

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

GnomAD4 genome AF: 0.00878 AC: 1336 AN: 152084 Hom.: 19 Cov.: 32 AF XY: 0.00935 AC XY: 695 AN XY: 74336

African (AFR) AF: 0.00229 AC: 95 AN: 41538

American (AMR) AF: 0.0182 AC: 277 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00347 AC: 12 AN: 3462

East Asian (EAS) AF: 0.0645 AC: 331 AN: 5128

South Asian (SAS) AF: 0.0205 AC: 99 AN: 4824

European-Finnish (FIN) AF: 0.00368 AC: 39 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.00686 AC: 466 AN: 67964

Other (OTH) AF: 0.00758 AC: 16 AN: 2110

Alfa AF: 0.00731 Hom.: 2

Bravo AF: 0.0109

Asia WGS AF: 0.0530 AC: 184 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.028
DANN	Benign	0.38
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs10503051; hg19: chr18-58893990;