5-166150614-A-G

Variant names:

• chr5-166150614-A-G
• rs844221
• ENST00000520075.2:n.252-4544A>G

Variant summary

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

The ENST00000520075.2(ENSG00000254171):​n.252-4544A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,104 control chromosomes in the GnomAD database, including 56,675 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 0.84 (56675 hom., cov: 31)
• Consequence: ENSG00000254171 ENST00000520075.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176
• Publications: 2 publications found

Genes affected

ENSG00000254171 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520075.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254171	ENST00000520075.2	TSL:3	n.252-4544A>G		intron	N/A
	ENSG00000254171	ENST00000752385.1		n.144-4544A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127761 AN: 151986 Hom.: 56673 Cov.: 31

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.832

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.877

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.992

Gnomad MID AF: 0.943

Gnomad NFE AF: 0.981

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.840 AC: 127791 AN: 152104 Hom.: 56675 Cov.: 31 AF XY: 0.842 AC XY: 62633 AN XY: 74366

African (AFR) AF: 0.533 AC: 22085 AN: 41402

American (AMR) AF: 0.833 AC: 12733 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3431 AN: 3472

East Asian (EAS) AF: 0.876 AC: 4510 AN: 5148

South Asian (SAS) AF: 0.978 AC: 4713 AN: 4820

European-Finnish (FIN) AF: 0.992 AC: 10538 AN: 10618

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.981 AC: 66749 AN: 68028

Other (OTH) AF: 0.871 AC: 1844 AN: 2116

Alfa AF: 0.942 Hom.: 46345

Bravo AF: 0.812

Asia WGS AF: 0.893 AC: 3107 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs844221; hg19: chr5-165577619;