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
• Publications: 2 publications found

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

African (AFR) AF: 0.667 AC: 27665 AN: 41490

American (AMR) AF: 0.567 AC: 8649 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.654 AC: 2268 AN: 3468

East Asian (EAS) AF: 0.723 AC: 3733 AN: 5162

South Asian (SAS) AF: 0.612 AC: 2943 AN: 4808

European-Finnish (FIN) AF: 0.445 AC: 4688 AN: 10546

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.560 AC: 38028 AN: 67936

Other (OTH) AF: 0.594 AC: 1257 AN: 2116

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
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs4553720; hg19: chr18-62170726;