rs1494671

Positions:

• chr5-124545158-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 0.481 in 151,888 control chromosomes in the GnomAD database, including 18,433 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 0.48 (18433 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.637 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: 0.481 AC: 73031 AN: 151770 Hom.: 18396 Cov.: 31

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.481 AC: 73110 AN: 151888 Hom.: 18433 Cov.: 31 AF XY: 0.472 AC XY: 35044 AN XY: 74242

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.276

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.451

Alfa AF: 0.453 Hom.: 32244

Bravo AF: 0.484

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1494671; hg19: chr5-123880851;