rs292411

chr5-163617908-A-Gchr5-163617908-A-T

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 0.448 in 133,300 control chromosomes in the GnomAD database, including 13,369 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 0.45 (13369 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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: 0.448 AC: 59688 AN: 133224 Hom.: 13370 Cov.: 23

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.455

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.486

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.448 AC: 59700 AN: 133300 Hom.: 13369 Cov.: 23 AF XY: 0.449 AC XY: 28979 AN XY: 64608

Gnomad4 AFR AF: 0.337

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.455

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.463

Gnomad4 OTH AF: 0.460

Alfa AF: 0.406 Hom.: 1614

Bravo AF: 0.423

Asia WGS AF: 0.588 AC: 2043 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.17
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs292411; hg19: chr5-163044914;