rs1870832

Variant names:

• chr6-88447308-G-A
• rs1870832

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 0.654 in 151,860 control chromosomes in the GnomAD database, including 32,811 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 0.65 (32811 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.418
• Publications: 10 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 (EAS) allele frequency at 95% confidence interval = 0.787 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: 0.654 AC: 99167 AN: 151742 Hom.: 32777 Cov.: 30

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.585

Gnomad EAS AF: 0.809

Gnomad SAS AF: 0.692

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.654 AC: 99253 AN: 151860 Hom.: 32811 Cov.: 30 AF XY: 0.661 AC XY: 49051 AN XY: 74208

African (AFR) AF: 0.686 AC: 28424 AN: 41414

American (AMR) AF: 0.738 AC: 11261 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 2028 AN: 3466

East Asian (EAS) AF: 0.808 AC: 4146 AN: 5132

South Asian (SAS) AF: 0.693 AC: 3331 AN: 4810

European-Finnish (FIN) AF: 0.675 AC: 7121 AN: 10542

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40648 AN: 67926

Other (OTH) AF: 0.684 AC: 1445 AN: 2112

Alfa AF: 0.622 Hom.: 99937

Bravo AF: 0.662

Asia WGS AF: 0.763 AC: 2651 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	1.1
DANN	Benign	0.27
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs1870832; hg19: chr6-89157027;