rs9321588

Variant names:

• chr6-137124222-C-T
• rs9321588

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 0.387 in 151,846 control chromosomes in the GnomAD database, including 11,697 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 (11697 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.488 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: 0.387 AC: 58783 AN: 151730 Hom.: 11691 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.387 AC: 58794 AN: 151846 Hom.: 11697 Cov.: 31 AF XY: 0.383 AC XY: 28392 AN XY: 74206

African (AFR) AF: 0.493 AC: 20424 AN: 41406

American (AMR) AF: 0.346 AC: 5283 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.475 AC: 1648 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1628 AN: 5162

South Asian (SAS) AF: 0.349 AC: 1683 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3033 AN: 10494

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.352 AC: 23895 AN: 67926

Other (OTH) AF: 0.373 AC: 787 AN: 2110

Alfa AF: 0.390 Hom.: 2260

Bravo AF: 0.394

Asia WGS AF: 0.301 AC: 1045 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs9321588; hg19: chr6-137445359;