rs1323619

Variant names:

• chr13-77513130-C-A
• rs1323619

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 0.364 in 152,054 control chromosomes in the GnomAD database, including 11,264 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 0.36 (11264 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 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: 0.365 AC: 55392 AN: 151932 Hom.: 11269 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.364 AC: 55402 AN: 152054 Hom.: 11264 Cov.: 32 AF XY: 0.360 AC XY: 26782 AN XY: 74310

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.490

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.398

Alfa AF: 0.455 Hom.: 32299

Bravo AF: 0.354

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.2
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1323619; hg19: chr13-78087265;