5-18173563-C-T

Variant names:

• chr5-18173563-C-T
• rs2443547

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 0.638 in 152,008 control chromosomes in the GnomAD database, including 33,075 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 0.64 (33075 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.878 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: 0.638 AC: 96872 AN: 151888 Hom.: 33011 Cov.: 32

Gnomad AFR AF: 0.885

Gnomad AMI AF: 0.639

Gnomad AMR AF: 0.630

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.702

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.445

Gnomad MID AF: 0.596

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.638 AC: 96991 AN: 152008 Hom.: 33075 Cov.: 32 AF XY: 0.634 AC XY: 47124 AN XY: 74290

African (AFR) AF: 0.885 AC: 36778 AN: 41536

American (AMR) AF: 0.630 AC: 9598 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1989 AN: 3468

East Asian (EAS) AF: 0.702 AC: 3632 AN: 5172

South Asian (SAS) AF: 0.656 AC: 3165 AN: 4826

European-Finnish (FIN) AF: 0.445 AC: 4689 AN: 10546

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35050 AN: 67904

Other (OTH) AF: 0.633 AC: 1334 AN: 2106

Alfa AF: 0.537 Hom.: 11434

Bravo AF: 0.660

Asia WGS AF: 0.675 AC: 2346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.56
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs2443547; hg19: chr5-18173672;