rs1390566

Variant names:

• chr5-18624372-C-T
• rs1390566

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 0.323 in 151,780 control chromosomes in the GnomAD database, including 8,326 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 0.32 (8326 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 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: 0.323 AC: 48977 AN: 151664 Hom.: 8312 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.323 AC: 49035 AN: 151780 Hom.: 8326 Cov.: 32 AF XY: 0.331 AC XY: 24518 AN XY: 74170

African (AFR) AF: 0.306 AC: 12686 AN: 41422

American (AMR) AF: 0.468 AC: 7134 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 935 AN: 3466

East Asian (EAS) AF: 0.405 AC: 2083 AN: 5144

South Asian (SAS) AF: 0.477 AC: 2298 AN: 4818

European-Finnish (FIN) AF: 0.312 AC: 3279 AN: 10512

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19553 AN: 67878

Other (OTH) AF: 0.336 AC: 707 AN: 2106

Alfa AF: 0.305 Hom.: 21307

Bravo AF: 0.331

Asia WGS AF: 0.443 AC: 1536 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.76
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs1390566; hg19: chr5-18624481;