rs1343930

chr13-65715203-A-G

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 0.1 in 151,922 control chromosomes in the GnomAD database, including 830 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 0.10 (830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.653

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.153 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: 0.100 AC: 15230 AN: 151804 Hom.: 824 Cov.: 32

Gnomad AFR AF: 0.0798

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.158

Gnomad ASJ AF: 0.0265

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.0985

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.0796

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

GnomAD4 genome AF: 0.100 AC: 15246 AN: 151922 Hom.: 830 Cov.: 32 AF XY: 0.102 AC XY: 7533 AN XY: 74214

Gnomad4 AFR AF: 0.0797

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0265

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.0986

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.0787

Alfa AF: 0.0988 Hom.: 138

Bravo AF: 0.0985

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.9
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343930; hg19: chr13-66289335;