rs1501680

Variant names:

• chr5-28281534-G-A
• rs1501680

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 0.31 in 152,056 control chromosomes in the GnomAD database, including 8,280 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 0.31 (8280 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 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: 0.310 AC: 47042 AN: 151940 Hom.: 8255 Cov.: 33

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.310 AC: 47111 AN: 152056 Hom.: 8280 Cov.: 33 AF XY: 0.310 AC XY: 23048 AN XY: 74330

African (AFR) AF: 0.414 AC: 17176 AN: 41476

American (AMR) AF: 0.334 AC: 5093 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 884 AN: 3466

East Asian (EAS) AF: 0.683 AC: 3527 AN: 5164

South Asian (SAS) AF: 0.292 AC: 1411 AN: 4830

European-Finnish (FIN) AF: 0.232 AC: 2450 AN: 10562

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15728 AN: 67968

Other (OTH) AF: 0.277 AC: 585 AN: 2114

Alfa AF: 0.263 Hom.: 1060

Bravo AF: 0.325

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	4.0
DANN	Benign	0.53
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1501680; hg19: chr5-28281641;