13-18737101-C-T

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 0.0718 in 152,144 control chromosomes in the GnomAD database, including 449 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 0.072 (449 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0718 AC: 10916 AN: 152026 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.0571

Gnomad AMI AF: 0.0670

Gnomad AMR AF: 0.0522

Gnomad ASJ AF: 0.0788

Gnomad EAS AF: 0.0332

Gnomad SAS AF: 0.0438

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0830

Gnomad OTH AF: 0.0657

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

GnomAD4 genome AF: 0.0718 AC: 10926 AN: 152144 Hom.: 449 Cov.: 32 AF XY: 0.0717 AC XY: 5332 AN XY: 74372

Gnomad4 AFR AF: 0.0572

Gnomad4 AMR AF: 0.0521

Gnomad4 ASJ AF: 0.0788

Gnomad4 EAS AF: 0.0333

Gnomad4 SAS AF: 0.0434

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.0830

Gnomad4 OTH AF: 0.0650

Alfa AF: 0.0301 Hom.: 21

Bravo AF: 0.0678

Asia WGS AF: 0.0330 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.3
Dann	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552416; hg19: chr13-19311241;