13-105394164-C-T

Variant names:

• chr13-105394164-C-T
• rs7324448

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 0.323 in 151,810 control chromosomes in the GnomAD database, including 8,285 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 0.32 (8285 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.419 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: 0.323 AC: 48963 AN: 151692 Hom.: 8273 Cov.: 30

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.306

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

GnomAD4 genome AF: 0.323 AC: 49012 AN: 151810 Hom.: 8285 Cov.: 30 AF XY: 0.325 AC XY: 24080 AN XY: 74180

Gnomad4 AFR AF: 0.424

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.303

Alfa AF: 0.278 Hom.: 6440

Bravo AF: 0.325

Asia WGS AF: 0.264 AC: 922 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.77
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7324448; hg19: chr13-106046514;