rs1336938

Positions:

• chr13-88918751-C-A

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 0.145 in 151,588 control chromosomes in the GnomAD database, including 2,047 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 0.14 (2047 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.201 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: 0.145 AC: 21952 AN: 151470 Hom.: 2046 Cov.: 31

Gnomad AFR AF: 0.0522

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.00310

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.119

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.145 AC: 21961 AN: 151588 Hom.: 2047 Cov.: 31 AF XY: 0.145 AC XY: 10762 AN XY: 74100

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.00311

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.125

Alfa AF: 0.168 Hom.: 413

Bravo AF: 0.128

Asia WGS AF: 0.0470 AC: 164 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.5
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1336938; hg19: chr13-89571005;