rs545245

Variant names:

• chr18-66649982-T-C
• rs545245

Your query was ambiguous. Multiple possible variants found:

• chr18-66649982-T-C
• chr18-66649982-T-G

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 0.308 in 151,884 control chromosomes in the GnomAD database, including 8,313 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 0.31 (8313 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.788
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.435 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: 0.308 AC: 46756 AN: 151766 Hom.: 8309 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.364

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.467

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.308 AC: 46782 AN: 151884 Hom.: 8313 Cov.: 31 AF XY: 0.314 AC XY: 23302 AN XY: 74244

African (AFR) AF: 0.123 AC: 5089 AN: 41480

American (AMR) AF: 0.303 AC: 4621 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1131 AN: 3472

East Asian (EAS) AF: 0.365 AC: 1870 AN: 5130

South Asian (SAS) AF: 0.451 AC: 2168 AN: 4806

European-Finnish (FIN) AF: 0.467 AC: 4916 AN: 10518

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.380 AC: 25836 AN: 67928

Other (OTH) AF: 0.335 AC: 705 AN: 2104

Alfa AF: 0.292 Hom.: 2751

Bravo AF: 0.283

Asia WGS AF: 0.384 AC: 1336 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.9
DANN	Benign	0.65
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs545245; hg19: chr18-64317219;