rs1895452

Variant names:

• chr5-56764568-T-A
• rs1895452

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 0.235 in 152,202 control chromosomes in the GnomAD database, including 5,555 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 0.23 (5555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 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: 0.235 AC: 35732 AN: 152084 Hom.: 5557 Cov.: 32

Gnomad AFR AF: 0.0680

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.00923

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.235 AC: 35714 AN: 152202 Hom.: 5555 Cov.: 32 AF XY: 0.226 AC XY: 16845 AN XY: 74420

African (AFR) AF: 0.0679 AC: 2820 AN: 41550

American (AMR) AF: 0.216 AC: 3302 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1400 AN: 3466

East Asian (EAS) AF: 0.00906 AC: 47 AN: 5188

South Asian (SAS) AF: 0.135 AC: 652 AN: 4828

European-Finnish (FIN) AF: 0.276 AC: 2925 AN: 10588

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.347 AC: 23561 AN: 67988

Other (OTH) AF: 0.280 AC: 592 AN: 2114

Alfa AF: 0.262 Hom.: 676

Bravo AF: 0.225

Asia WGS AF: 0.0760 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.1
DANN	Benign	0.81
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs1895452; hg19: chr5-56060395; COSMIC: COSV60135531;