rs1417205

chr13-47324744-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 0.126 in 152,008 control chromosomes in the GnomAD database, including 2,156 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 0.13 (2156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 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: 0.126 AC: 19169 AN: 151890 Hom.: 2157 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.0655

Gnomad EAS AF: 0.0567

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0464

Gnomad MID AF: 0.0732

Gnomad NFE AF: 0.0516

Gnomad OTH AF: 0.115

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

GnomAD4 genome AF: 0.126 AC: 19187 AN: 152008 Hom.: 2156 Cov.: 32 AF XY: 0.125 AC XY: 9261 AN XY: 74332

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.0929

Gnomad4 ASJ AF: 0.0655

Gnomad4 EAS AF: 0.0569

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.0464

Gnomad4 NFE AF: 0.0516

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0620 Hom.: 348

Bravo AF: 0.136

Asia WGS AF: 0.0890 AC: 311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	7.5
Dann	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1417205; hg19: chr13-47898879;