rs9567354

Variant names:

• chr13-44066859-T-C
• rs9567354

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 0.196 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0574 AC: 2383 AN: 41536

American (AMR) AF: 0.122 AC: 1872 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 589 AN: 3468

East Asian (EAS) AF: 0.295 AC: 1523 AN: 5164

South Asian (SAS) AF: 0.275 AC: 1321 AN: 4810

European-Finnish (FIN) AF: 0.336 AC: 3553 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17952 AN: 67980

Other (OTH) AF: 0.168 AC: 355 AN: 2114

Alfa AF: 0.215 Hom.: 1751

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

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