rs9400393

Variant names:

• chr6-110482811-T-C
• rs9400393

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.366 in 152,186 control chromosomes in the GnomAD database, including 11,485 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 0.37 (11485 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.714
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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: 0.366 AC: 55637 AN: 152068 Hom.: 11473 Cov.: 33

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.366 AC: 55680 AN: 152186 Hom.: 11485 Cov.: 33 AF XY: 0.374 AC XY: 27830 AN XY: 74392

African (AFR) AF: 0.186 AC: 7735 AN: 41540

American (AMR) AF: 0.459 AC: 7018 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1022 AN: 3470

East Asian (EAS) AF: 0.510 AC: 2635 AN: 5164

South Asian (SAS) AF: 0.445 AC: 2149 AN: 4826

European-Finnish (FIN) AF: 0.525 AC: 5550 AN: 10574

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.417 AC: 28362 AN: 68000

Other (OTH) AF: 0.353 AC: 746 AN: 2114

Alfa AF: 0.396 Hom.: 37989

Bravo AF: 0.353

Asia WGS AF: 0.485 AC: 1686 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs9400393; hg19: chr6-110804014; COSMIC: COSV73909070;