rs9271378

Positions:

• chr6-32619523-A-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 0.46 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;