rs1494671

Variant names:

• chr5-124545158-A-G
• rs1494671

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.644 AC: 26653 AN: 41406

American (AMR) AF: 0.335 AC: 5109 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1554 AN: 3468

East Asian (EAS) AF: 0.276 AC: 1425 AN: 5156

South Asian (SAS) AF: 0.349 AC: 1676 AN: 4808

European-Finnish (FIN) AF: 0.409 AC: 4307 AN: 10542

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30858 AN: 67934

Other (OTH) AF: 0.451 AC: 952 AN: 2110

Alfa AF: 0.463 Hom.: 52779

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
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1494671; hg19: chr5-123880851;