rs1335485

Positions:

• chr13-88363678-G-A
• chr13-88363678-G-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 0.716 in 151,938 control chromosomes in the GnomAD database, including 39,226 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 0.72 (39226 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.158

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.786 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: 0.717 AC: 108796 AN: 151822 Hom.: 39209 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.629

Gnomad FIN AF: 0.675

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.730

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

GnomAD4 genome AF: 0.716 AC: 108859 AN: 151938 Hom.: 39226 Cov.: 31 AF XY: 0.715 AC XY: 53052 AN XY: 74246

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.797

Gnomad4 ASJ AF: 0.699

Gnomad4 EAS AF: 0.598

Gnomad4 SAS AF: 0.628

Gnomad4 FIN AF: 0.675

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.731

Alfa AF: 0.708 Hom.: 8253

Bravo AF: 0.725

Asia WGS AF: 0.633 AC: 2197 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1335485; hg19: chr13-89015933;