rs1341622

Variant names:

• chr13-54530436-G-A
• rs1341622

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 0.842 in 152,032 control chromosomes in the GnomAD database, including 54,038 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 0.84 (54038 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.914 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: 0.842 AC: 127863 AN: 151916 Hom.: 53982 Cov.: 31

Gnomad AFR AF: 0.921

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.852

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.842 AC: 127980 AN: 152032 Hom.: 54038 Cov.: 31 AF XY: 0.836 AC XY: 62121 AN XY: 74300

Gnomad4 AFR AF: 0.921

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.742

Gnomad4 SAS AF: 0.853

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.827

Gnomad4 OTH AF: 0.837

Alfa AF: 0.834 Hom.: 20352

Bravo AF: 0.843

Asia WGS AF: 0.829 AC: 2877 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1341622; hg19: chr13-55104571;