rs9321282

Variant names:

• chr6-131348234-T-C
• rs9321282
• ENST00000702750.2:n.304-36955A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000702750.2(ENSG00000290067):​n.304-36955A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 152,114 control chromosomes in the GnomAD database, including 4,079 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 0.22 (4079 hom., cov: 32)
• Consequence: ENSG00000290067 ENST00000702750.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 1 publications found

Genes affected

ENSG00000290067 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.307 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
ENSG00000290067	ENST00000702750.2	n.304-36955A>G		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771190.1	n.293-36955A>G		intron_variant	Intron 3 of 4
ENSG00000290067	ENST00000771191.1	n.450+9296A>G		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33869 AN: 151998 Hom.: 4072 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.0890

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.223 AC: 33902 AN: 152114 Hom.: 4079 Cov.: 32 AF XY: 0.222 AC XY: 16517 AN XY: 74362

African (AFR) AF: 0.311 AC: 12907 AN: 41466

American (AMR) AF: 0.256 AC: 3906 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 737 AN: 3470

East Asian (EAS) AF: 0.0896 AC: 464 AN: 5178

South Asian (SAS) AF: 0.198 AC: 953 AN: 4810

European-Finnish (FIN) AF: 0.194 AC: 2053 AN: 10582

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12273 AN: 68018

Other (OTH) AF: 0.201 AC: 425 AN: 2112

Alfa AF: 0.193 Hom.: 1480

Bravo AF: 0.230

Asia WGS AF: 0.130 AC: 452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.40
DANN	Benign	0.33
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs9321282; hg19: chr6-131669374;