9-5204404-C-T

Variant names:

• chr9-5204404-C-T
• rs6476948

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 0.306 in 151,892 control chromosomes in the GnomAD database, including 7,276 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 0.31 (7276 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.427

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.353 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: 0.305 AC: 46350 AN: 151774 Hom.: 7263 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.306 AC: 46410 AN: 151892 Hom.: 7276 Cov.: 32 AF XY: 0.310 AC XY: 22978 AN XY: 74222

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.299

Alfa AF: 0.262 Hom.: 2432

Bravo AF: 0.298

Asia WGS AF: 0.314 AC: 1087 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.19
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6476948; hg19: chr9-5204404; COSMIC: COSV60323521;