rs1584896

Variant names:

• chr6-80696914-A-G
• rs1584896

Your query was ambiguous. Multiple possible variants found:

• chr6-80696914-A-G
• chr6-80696914-A-T

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 0.394 in 151,996 control chromosomes in the GnomAD database, including 12,774 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 0.39 (12774 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.836
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 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: 0.395 AC: 59919 AN: 151878 Hom.: 12777 Cov.: 31

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.394 AC: 59920 AN: 151996 Hom.: 12774 Cov.: 31 AF XY: 0.390 AC XY: 28999 AN XY: 74286

African (AFR) AF: 0.224 AC: 9299 AN: 41510

American (AMR) AF: 0.461 AC: 7028 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.498 AC: 1727 AN: 3470

East Asian (EAS) AF: 0.318 AC: 1639 AN: 5154

South Asian (SAS) AF: 0.279 AC: 1345 AN: 4818

European-Finnish (FIN) AF: 0.451 AC: 4760 AN: 10558

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.480 AC: 32644 AN: 67938

Other (OTH) AF: 0.444 AC: 935 AN: 2106

Alfa AF: 0.418 Hom.: 1821

Bravo AF: 0.391

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.9
DANN	Benign	0.73
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs1584896; hg19: chr6-81406631;