rs9398840

Variant names:

• chr6-127348599-G-A
• rs9398840

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;