chr13-26708547-G-A

Position:

• chr13-26708547-G-A

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 0.417 in 146,186 control chromosomes in the GnomAD database, including 13,106 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 0.42 (13106 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.417 AC: 60973 AN: 146070 Hom.: 13098 Cov.: 28

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.417 AC: 61001 AN: 146186 Hom.: 13106 Cov.: 28 AF XY: 0.420 AC XY: 29822 AN XY: 71076

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.505

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.454

Alfa AF: 0.456 Hom.: 16171

Bravo AF: 0.390

Asia WGS AF: 0.440 AC: 1529 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4771006; hg19: chr13-27282684; COSMIC: COSV53406226;