13-104178871-T-C

Variant names:

• chr13-104178871-T-C
• rs1923862

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;