rs1895302

Variant names:

• chr5-170115596-C-T
• rs1895302

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 0.471 in 152,094 control chromosomes in the GnomAD database, including 18,671 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 0.47 (18671 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.581 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: 0.471 AC: 71590 AN: 151976 Hom.: 18665 Cov.: 33

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.591

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.471 AC: 71601 AN: 152094 Hom.: 18671 Cov.: 33 AF XY: 0.469 AC XY: 34827 AN XY: 74330

African (AFR) AF: 0.243 AC: 10085 AN: 41476

American (AMR) AF: 0.591 AC: 9031 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3470

East Asian (EAS) AF: 0.405 AC: 2099 AN: 5178

South Asian (SAS) AF: 0.570 AC: 2745 AN: 4820

European-Finnish (FIN) AF: 0.409 AC: 4329 AN: 10572

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.582 AC: 39550 AN: 67986

Other (OTH) AF: 0.503 AC: 1061 AN: 2110

Alfa AF: 0.593 Hom.: 16146

Bravo AF: 0.475

Asia WGS AF: 0.490 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.061
DANN	Benign	0.35
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1895302; hg19: chr5-169542600;