rs9369898

Positions:

• chr6-49414480-G-A
• chr6-49414480-G-C

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 0.589 in 150,244 control chromosomes in the GnomAD database, including 26,368 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 0.59 (26368 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.632 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: 0.589 AC: 88477 AN: 150148 Hom.: 26347 Cov.: 28

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.604

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.589 AC: 88533 AN: 150244 Hom.: 26368 Cov.: 28 AF XY: 0.584 AC XY: 42721 AN XY: 73202

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.436

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.462

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.604

Gnomad4 NFE AF: 0.626

Gnomad4 OTH AF: 0.553

Alfa AF: 0.595 Hom.: 3207

Bravo AF: 0.568

Asia WGS AF: 0.548 AC: 1908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.22
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9369898; hg19: chr6-49382193;