chr18-66649298-T-C

Variant names:

• chr18-66649298-T-C
• rs556372

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 151,904 control chromosomes in the GnomAD database, including 8,308 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 (8308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 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: 46760 AN: 151786 Hom.: 8304 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.384

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.326

Gnomad EAS AF: 0.360

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.468

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.380

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.308 AC: 46786 AN: 151904 Hom.: 8308 Cov.: 32 AF XY: 0.314 AC XY: 23300 AN XY: 74228

African (AFR) AF: 0.123 AC: 5099 AN: 41534

American (AMR) AF: 0.304 AC: 4633 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.326 AC: 1130 AN: 3468

East Asian (EAS) AF: 0.361 AC: 1857 AN: 5148

South Asian (SAS) AF: 0.452 AC: 2171 AN: 4802

European-Finnish (FIN) AF: 0.468 AC: 4904 AN: 10488

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

European-Non Finnish (NFE) AF: 0.381 AC: 25839 AN: 67906

Other (OTH) AF: 0.336 AC: 709 AN: 2110

Alfa AF: 0.346 Hom.: 12230

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	-0.92
CADD	Benign	2.8
DANN	Benign	0.75
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs556372; hg19: chr18-64316535;