18-64503491-T-C

Variant names:

• chr18-64503491-T-C
• rs4553720

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 0.592 in 151,992 control chromosomes in the GnomAD database, including 26,988 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 0.59 (26988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.990

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.704 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: 0.592 AC: 89901 AN: 151874 Hom.: 26949 Cov.: 32

Gnomad AFR AF: 0.666

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.654

Gnomad EAS AF: 0.723

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.636

Gnomad NFE AF: 0.560

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.592 AC: 89994 AN: 151992 Hom.: 26988 Cov.: 32 AF XY: 0.587 AC XY: 43554 AN XY: 74248

Gnomad4 AFR AF: 0.667 AC: 0.666787 AN: 0.666787

Gnomad4 AMR AF: 0.567 AC: 0.566702 AN: 0.566702

Gnomad4 ASJ AF: 0.654 AC: 0.653979 AN: 0.653979

Gnomad4 EAS AF: 0.723 AC: 0.723169 AN: 0.723169

Gnomad4 SAS AF: 0.612 AC: 0.612105 AN: 0.612105

Gnomad4 FIN AF: 0.445 AC: 0.444529 AN: 0.444529

Gnomad4 NFE AF: 0.560 AC: 0.559762 AN: 0.559762

Gnomad4 OTH AF: 0.594 AC: 0.594045 AN: 0.594045

Alfa AF: 0.580 Hom.: 60568

Bravo AF: 0.606

Asia WGS AF: 0.669 AC: 2313 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.9
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4553720; hg19: chr18-62170726;