rs9400554

Variant names:

• chr6-95552246-C-T
• rs9400554

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 0.466 in 151,866 control chromosomes in the GnomAD database, including 16,606 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 0.47 (16606 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0460

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.527 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: 0.466 AC: 70763 AN: 151748 Hom.: 16596 Cov.: 31

Gnomad AFR AF: 0.472

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.528

Gnomad EAS AF: 0.506

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.466 AC: 70808 AN: 151866 Hom.: 16606 Cov.: 31 AF XY: 0.466 AC XY: 34557 AN XY: 74212

Gnomad4 AFR AF: 0.472

Gnomad4 AMR AF: 0.425

Gnomad4 ASJ AF: 0.528

Gnomad4 EAS AF: 0.506

Gnomad4 SAS AF: 0.545

Gnomad4 FIN AF: 0.462

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.493

Alfa AF: 0.467 Hom.: 22065

Bravo AF: 0.460

Asia WGS AF: 0.555 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
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: rs9400554; hg19: chr6-96000122;