rs9567354

Variant names:

• chr13-44066859-T-C
• rs9567354

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 0.196 in 152,154 control chromosomes in the GnomAD database, including 3,673 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 0.20 (3673 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.196 AC: 29807 AN: 152036 Hom.: 3673 Cov.: 32

Gnomad AFR AF: 0.0574

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.196 AC: 29801 AN: 152154 Hom.: 3673 Cov.: 32 AF XY: 0.199 AC XY: 14808 AN XY: 74374

Gnomad4 AFR AF: 0.0574

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.336

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.168

Alfa AF: 0.215 Hom.: 1163

Bravo AF: 0.172

Asia WGS AF: 0.221 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.95
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9567354; hg19: chr13-44640995; COSMIC: COSV69348398;