rs9398840

Positions:

• chr6-127348599-G-A
• chr6-127348599-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 0.739 in 152,038 control chromosomes in the GnomAD database, including 41,678 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 0.74 (41678 hom., cov: 32)
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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: 0.739 AC: 112301 AN: 151920 Hom.: 41650 Cov.: 32

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.754

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.619

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.739 AC: 112379 AN: 152038 Hom.: 41678 Cov.: 32 AF XY: 0.734 AC XY: 54529 AN XY: 74278

Gnomad4 AFR AF: 0.721

Gnomad4 AMR AF: 0.754

Gnomad4 ASJ AF: 0.762

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.619

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.758

Alfa AF: 0.749 Hom.: 83502

Bravo AF: 0.744

Asia WGS AF: 0.692 AC: 2409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9398840; hg19: chr6-127669744;