rs9275371

Positions:

• chr6-32700519-T-C
• chr6-32700519-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.292 in 151,218 control chromosomes in the GnomAD database, including 7,064 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 0.29 (7064 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.387 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.32700519T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44095 AN: 151100 Hom.: 7048 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.292 AC: 44156 AN: 151218 Hom.: 7064 Cov.: 32 AF XY: 0.302 AC XY: 22308 AN XY: 73908

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.396

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.287

Alfa AF: 0.263 Hom.: 2625

Bravo AF: 0.295

Asia WGS AF: 0.276 AC: 966 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	7.4
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9275371; hg19: chr6-32668296;