chr13-109744675-T-C

Variant names:

• chr13-109744675-T-C
• rs1556223

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 0.575 in 152,060 control chromosomes in the GnomAD database, including 25,480 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 0.58 (25480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.672 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: 0.575 AC: 87427 AN: 151940 Hom.: 25469 Cov.: 33

Gnomad AFR AF: 0.485

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.575 AC: 87475 AN: 152060 Hom.: 25480 Cov.: 33 AF XY: 0.577 AC XY: 42876 AN XY: 74308

Gnomad4 AFR AF: 0.485

Gnomad4 AMR AF: 0.683

Gnomad4 ASJ AF: 0.621

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.581

Alfa AF: 0.605 Hom.: 28069

Bravo AF: 0.579

Asia WGS AF: 0.536 AC: 1867 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.028
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556223; hg19: chr13-110397022;