18-66152079-G-T

Variant names:

• chr18-66152079-G-T
• rs10503104

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 0.892 in 151,882 control chromosomes in the GnomAD database, including 61,314 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 0.89 (61314 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.978 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: 0.892 AC: 135334 AN: 151764 Hom.: 61274 Cov.: 30

Gnomad AFR AF: 0.737

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.975

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.938

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.984

Gnomad OTH AF: 0.907

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

GnomAD4 genome AF: 0.892 AC: 135429 AN: 151882 Hom.: 61314 Cov.: 30 AF XY: 0.889 AC XY: 66053 AN XY: 74280

African (AFR) AF: 0.737 AC: 30538 AN: 41408

American (AMR) AF: 0.912 AC: 13903 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.975 AC: 3383 AN: 3470

East Asian (EAS) AF: 0.695 AC: 3580 AN: 5150

South Asian (SAS) AF: 0.869 AC: 4191 AN: 4822

European-Finnish (FIN) AF: 0.938 AC: 9938 AN: 10592

Middle Eastern (MID) AF: 0.956 AC: 281 AN: 294

European-Non Finnish (NFE) AF: 0.984 AC: 66790 AN: 67882

Other (OTH) AF: 0.909 AC: 1922 AN: 2114

Alfa AF: 0.953 Hom.: 32930

Bravo AF: 0.883

Asia WGS AF: 0.804 AC: 2794 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.57
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10503104; hg19: chr18-63819315;