chr6-88584026-A-G

Variant names:

• chr6-88584026-A-G
• rs12527253

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 0.214 in 152,132 control chromosomes in the GnomAD database, including 4,562 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 0.21 (4562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.375 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: 0.214 AC: 32548 AN: 152014 Hom.: 4562 Cov.: 32

Gnomad AFR AF: 0.0566

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.0848

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.214 AC: 32548 AN: 152132 Hom.: 4562 Cov.: 32 AF XY: 0.218 AC XY: 16196 AN XY: 74360

African (AFR) AF: 0.0565 AC: 2347 AN: 41550

American (AMR) AF: 0.176 AC: 2693 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 994 AN: 3468

East Asian (EAS) AF: 0.0844 AC: 437 AN: 5178

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4818

European-Finnish (FIN) AF: 0.368 AC: 3888 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19615 AN: 67960

Other (OTH) AF: 0.199 AC: 422 AN: 2116

Alfa AF: 0.250 Hom.: 15246

Bravo AF: 0.189

Asia WGS AF: 0.226 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.1
DANN	Benign	0.67
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs12527253; hg19: chr6-89293745;