9-5204404-C-T

Variant names:

• chr9-5204404-C-T
• rs6476948

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 0.306 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.358 AC: 14819 AN: 41394

American (AMR) AF: 0.287 AC: 4380 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 871 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1338 AN: 5170

South Asian (SAS) AF: 0.341 AC: 1635 AN: 4796

European-Finnish (FIN) AF: 0.352 AC: 3709 AN: 10534

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18709 AN: 67964

Other (OTH) AF: 0.299 AC: 630 AN: 2106

Alfa AF: 0.264 Hom.: 2766

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
PhyloP100		-0.43

Splicing

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

Other links and lift over

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