13-104178871-T-C

Position:

• chr13-104178871-T-C

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 0.703 in 151,550 control chromosomes in the GnomAD database, including 37,464 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 0.70 (37464 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.769 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: 0.703 AC: 106453 AN: 151434 Hom.: 37435 Cov.: 31

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.789

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.753

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.703 AC: 106519 AN: 151550 Hom.: 37464 Cov.: 31 AF XY: 0.706 AC XY: 52261 AN XY: 74036

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.753

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.709

Alfa AF: 0.702 Hom.: 16853

Bravo AF: 0.702

Asia WGS AF: 0.763 AC: 2650 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.59
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923862; hg19: chr13-104831221;