rs1584897

Variant names:

• chr6-80696945-G-A
• rs1584897

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 0.147 in 152,040 control chromosomes in the GnomAD database, including 1,674 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 0.15 (1674 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.163 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: 0.147 AC: 22335 AN: 151924 Hom.: 1676 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.241

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0804

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.147 AC: 22335 AN: 152040 Hom.: 1674 Cov.: 32 AF XY: 0.146 AC XY: 10871 AN XY: 74298

African (AFR) AF: 0.118 AC: 4883 AN: 41484

American (AMR) AF: 0.162 AC: 2469 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 507 AN: 3470

East Asian (EAS) AF: 0.0806 AC: 416 AN: 5160

South Asian (SAS) AF: 0.163 AC: 785 AN: 4816

European-Finnish (FIN) AF: 0.136 AC: 1433 AN: 10570

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11263 AN: 67972

Other (OTH) AF: 0.146 AC: 308 AN: 2114

Alfa AF: 0.163 Hom.: 3813

Bravo AF: 0.151

Asia WGS AF: 0.102 AC: 355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.4
DANN	Benign	0.44
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs1584897; hg19: chr6-81406662; COSMIC: COSV69407865;