13-105394164-C-T

Variant names:

• chr13-105394164-C-T
• rs7324448

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 0.323 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• 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

African (AFR) AF: 0.424 AC: 17558 AN: 41370

American (AMR) AF: 0.307 AC: 4680 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 955 AN: 3466

East Asian (EAS) AF: 0.280 AC: 1436 AN: 5136

South Asian (SAS) AF: 0.247 AC: 1186 AN: 4804

European-Finnish (FIN) AF: 0.362 AC: 3810 AN: 10538

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18471 AN: 67938

Other (OTH) AF: 0.303 AC: 639 AN: 2112

Alfa AF: 0.285 Hom.: 9738

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs7324448; hg19: chr13-106046514;