18-60248736-T-C

Variant names:

• chr18-60248736-T-C
• rs752720

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 0.518 in 151,990 control chromosomes in the GnomAD database, including 21,099 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 0.52 (21099 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 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: 0.518 AC: 78674 AN: 151872 Hom.: 21076 Cov.: 32

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.540

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.518 AC: 78734 AN: 151990 Hom.: 21099 Cov.: 32 AF XY: 0.512 AC XY: 38010 AN XY: 74284

African (AFR) AF: 0.624 AC: 25864 AN: 41434

American (AMR) AF: 0.387 AC: 5908 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3466

East Asian (EAS) AF: 0.229 AC: 1183 AN: 5172

South Asian (SAS) AF: 0.610 AC: 2941 AN: 4818

European-Finnish (FIN) AF: 0.447 AC: 4718 AN: 10550

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35010 AN: 67958

Other (OTH) AF: 0.488 AC: 1031 AN: 2114

Alfa AF: 0.505 Hom.: 32298

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.46
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs752720; hg19: chr18-57915969;