rs881152

Variant names:

• chr5-172771552-G-A
• rs881152
• ENST00000523005.1:n.70-5940G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-172771552-G-A
• chr5-172771552-G-C

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.70-5940G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 152,128 control chromosomes in the GnomAD database, including 3,865 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 0.22 (3865 hom., cov: 33)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.664

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.243 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
ENSG00000253736	ENST00000523005.1	n.70-5940G>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33742 AN: 152012 Hom.: 3866 Cov.: 33

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.0531

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.246

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.222 AC: 33742 AN: 152128 Hom.: 3865 Cov.: 33 AF XY: 0.220 AC XY: 16345 AN XY: 74386

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.0533

Gnomad4 SAS AF: 0.213

Gnomad4 FIN AF: 0.247

Gnomad4 NFE AF: 0.246

Gnomad4 OTH AF: 0.181

Alfa AF: 0.167 Hom.: 432

Bravo AF: 0.212

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs881152; hg19: chr5-172198555;