rs1343930

Variant names:

• chr13-65715203-A-G
• rs1343930

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0797 AC: 3310 AN: 41536

American (AMR) AF: 0.159 AC: 2410 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.0265 AC: 92 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5170

South Asian (SAS) AF: 0.0986 AC: 476 AN: 4830

European-Finnish (FIN) AF: 0.126 AC: 1337 AN: 10598

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.109 AC: 7425 AN: 67818

Other (OTH) AF: 0.0787 AC: 166 AN: 2108

Alfa AF: 0.0932 Hom.: 235

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
PhyloP100		0.65

Splicing

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

Other links and lift over

dbSNP: rs1343930; hg19: chr13-66289335;