13-105404308-A-T

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 0.629 in 151,830 control chromosomes in the GnomAD database, including 31,523 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 0.63 (31523 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95317 AN: 151710 Hom.: 31459 Cov.: 31

Gnomad AFR AF: 0.834

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.453

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.629 AC: 95445 AN: 151830 Hom.: 31523 Cov.: 31 AF XY: 0.632 AC XY: 46879 AN XY: 74182

Gnomad4 AFR AF: 0.834

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.453

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.591

Alfa AF: 0.585 Hom.: 3173

Bravo AF: 0.638

Asia WGS AF: 0.635 AC: 2206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.5
Dann	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2181953; hg19: chr13-106056658;