rs9393553

Variant names:

• chr6-24401426-G-T
• rs9393553

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 0.271 in 151,728 control chromosomes in the GnomAD database, including 6,048 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 0.27 (6048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.453 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: 0.271 AC: 41124 AN: 151610 Hom.: 6025 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.243

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

GnomAD4 genome AF: 0.271 AC: 41180 AN: 151728 Hom.: 6048 Cov.: 32 AF XY: 0.278 AC XY: 20586 AN XY: 74122

African (AFR) AF: 0.208 AC: 8595 AN: 41356

American (AMR) AF: 0.396 AC: 6043 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 607 AN: 3464

East Asian (EAS) AF: 0.469 AC: 2418 AN: 5160

South Asian (SAS) AF: 0.356 AC: 1708 AN: 4796

European-Finnish (FIN) AF: 0.294 AC: 3087 AN: 10498

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17748 AN: 67902

Other (OTH) AF: 0.245 AC: 515 AN: 2100

Alfa AF: 0.267 Hom.: 20404

Bravo AF: 0.276

Asia WGS AF: 0.384 AC: 1334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.3
DANN	Benign	0.74
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs9393553; hg19: chr6-24401654;