5-166150614-A-G

Variant names:

• chr5-166150614-A-G
• rs844221
• ENST00000520075.1:n.252-4544A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000520075.1(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 ENST00000520075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

Genes affected

ENSG00000254171 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.975 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
ENSG00000254171	ENST00000520075.1	n.252-4544A>G		intron_variant	Intron 2 of 2	3

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

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.833

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.978

Gnomad4 FIN AF: 0.992

Gnomad4 NFE AF: 0.981

Gnomad4 OTH AF: 0.871

Alfa AF: 0.933 Hom.: 22987

Bravo AF: 0.812

Asia WGS AF: 0.893 AC: 3107 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	1.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs844221; hg19: chr5-165577619;