chr18-4721359-C-T

Variant names:

• chr18-4721359-C-T
• rs1557305

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 0.34 in 151,904 control chromosomes in the GnomAD database, including 9,338 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 0.34 (9338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51614 AN: 151786 Hom.: 9345 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.339

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

GnomAD4 genome AF: 0.340 AC: 51630 AN: 151904 Hom.: 9338 Cov.: 32 AF XY: 0.344 AC XY: 25548 AN XY: 74218

African (AFR) AF: 0.229 AC: 9479 AN: 41422

American (AMR) AF: 0.408 AC: 6220 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3466

East Asian (EAS) AF: 0.502 AC: 2583 AN: 5146

South Asian (SAS) AF: 0.471 AC: 2266 AN: 4816

European-Finnish (FIN) AF: 0.347 AC: 3652 AN: 10532

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25392 AN: 67952

Other (OTH) AF: 0.337 AC: 711 AN: 2110

Alfa AF: 0.359 Hom.: 31492

Bravo AF: 0.337

Asia WGS AF: 0.434 AC: 1510 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.012
DANN	Benign	0.52
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1557305; hg19: chr18-4721359;