rs60271

Variant names:

• chr5-104742532-A-C
• rs60271
• ENST00000503650.1:n.328+144326T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000503650.1(ENSG00000251574):​n.328+144326T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.771 in 152,026 control chromosomes in the GnomAD database, including 46,444 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 0.77 (46444 hom., cov: 31)
• Consequence: ENSG00000251574 ENST00000503650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.881
• Publications: 4 publications found

Genes affected

ENSG00000251574 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000503650.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379109	NR_188304.1		n.175+20748T>G		intron	N/A
	LOC105379109	NR_188305.1		n.295+20748T>G		intron	N/A
	LOC105379109	NR_188306.1		n.175+20748T>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000251574	ENST00000503650.1	TSL:3	n.328+144326T>G		intron	N/A
	ENSG00000251574	ENST00000505824.6	TSL:3	n.307+20748T>G		intron	N/A
	ENSG00000251574	ENST00000506976.6	TSL:3	n.203+20748T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.771 AC: 117136 AN: 151908 Hom.: 46381 Cov.: 31

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.784

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.930

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.771 AC: 117257 AN: 152026 Hom.: 46444 Cov.: 31 AF XY: 0.772 AC XY: 57351 AN XY: 74272

African (AFR) AF: 0.942 AC: 39106 AN: 41498

American (AMR) AF: 0.784 AC: 11958 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2364 AN: 3472

East Asian (EAS) AF: 0.931 AC: 4796 AN: 5150

South Asian (SAS) AF: 0.620 AC: 2991 AN: 4826

European-Finnish (FIN) AF: 0.726 AC: 7677 AN: 10574

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 46016 AN: 67944

Other (OTH) AF: 0.770 AC: 1625 AN: 2110

Alfa AF: 0.712 Hom.: 28810

Bravo AF: 0.790

Asia WGS AF: 0.795 AC: 2766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.73
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs60271; hg19: chr5-104078233;