13-111556870-C-T

Variant names:

• chr13-111556870-C-T
• rs4771759

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 0.3 in 152,092 control chromosomes in the GnomAD database, including 7,142 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 0.30 (7142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 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: 0.300 AC: 45634 AN: 151974 Hom.: 7143 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.300 AC: 45640 AN: 152092 Hom.: 7142 Cov.: 32 AF XY: 0.307 AC XY: 22834 AN XY: 74344

Gnomad4 AFR AF: 0.217

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.348

Gnomad4 EAS AF: 0.427

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.312

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.316

Alfa AF: 0.313 Hom.: 12853

Bravo AF: 0.296

Asia WGS AF: 0.413 AC: 1437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.10
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4771759; hg19: chr13-112209217;