rs1870584

Variant names:

• chr17-12144227-A-G
• rs1870584

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 0.398 in 151,896 control chromosomes in the GnomAD database, including 12,285 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 0.40 (12285 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.567 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: 0.398 AC: 60344 AN: 151778 Hom.: 12274 Cov.: 32

Gnomad AFR AF: 0.348

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.401

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

GnomAD4 genome AF: 0.398 AC: 60386 AN: 151896 Hom.: 12285 Cov.: 32 AF XY: 0.400 AC XY: 29681 AN XY: 74208

African (AFR) AF: 0.348 AC: 14431 AN: 41418

American (AMR) AF: 0.471 AC: 7192 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1494 AN: 3472

East Asian (EAS) AF: 0.585 AC: 3001 AN: 5134

South Asian (SAS) AF: 0.398 AC: 1914 AN: 4808

European-Finnish (FIN) AF: 0.383 AC: 4042 AN: 10542

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27070 AN: 67948

Other (OTH) AF: 0.404 AC: 848 AN: 2098

Alfa AF: 0.396 Hom.: 11510

Bravo AF: 0.403

Asia WGS AF: 0.525 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.77
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs1870584; hg19: chr17-12047544;