chr13-104557564-C-G

Position:

• chr13-104557564-C-G

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 0.41 in 152,012 control chromosomes in the GnomAD database, including 14,445 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 0.41 (14445 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.541

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.615 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: 0.410 AC: 62330 AN: 151894 Hom.: 14431 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.410 AC: 62378 AN: 152012 Hom.: 14445 Cov.: 32 AF XY: 0.399 AC XY: 29678 AN XY: 74300

Gnomad4 AFR AF: 0.621

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.236

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.393

Alfa AF: 0.388 Hom.: 1559

Bravo AF: 0.424

Asia WGS AF: 0.202 AC: 704 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.3
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs892535; hg19: chr13-105209915;