rs9271378

Variant names:

• chr6-32619523-A-G
• rs9271378

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 0.46 in 151,436 control chromosomes in the GnomAD database, including 16,521 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 0.46 (16521 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.477 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: 0.460 AC: 69655 AN: 151318 Hom.: 16518 Cov.: 29

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.460 AC: 69680 AN: 151436 Hom.: 16521 Cov.: 29 AF XY: 0.452 AC XY: 33466 AN XY: 73966

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.481

Gnomad4 OTH AF: 0.488

Alfa AF: 0.481 Hom.: 2186

Bravo AF: 0.464

Asia WGS AF: 0.280 AC: 972 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.2
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9271378; hg19: chr6-32587300;