chr5-172771552-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000523005.1. 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
	ENSG00000253736	ENST00000523005.1	TSL:3	n.70-5940G>A		intron	N/A
	ENSG00000253736	ENST00000792668.1		n.-75G>A		upstream_gene	N/A

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

African (AFR) AF: 0.222 AC: 9232 AN: 41502

American (AMR) AF: 0.180 AC: 2760 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 472 AN: 3470

East Asian (EAS) AF: 0.0533 AC: 275 AN: 5162

South Asian (SAS) AF: 0.213 AC: 1025 AN: 4822

European-Finnish (FIN) AF: 0.247 AC: 2618 AN: 10612

Middle Eastern (MID) AF: 0.130 AC: 38 AN: 292

European-Non Finnish (NFE) AF: 0.246 AC: 16696 AN: 67948

Other (OTH) AF: 0.181 AC: 382 AN: 2108

Alfa AF: 0.188 Hom.: 1001

Bravo AF: 0.212

Asia WGS AF: 0.127 AC: 442 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.5
DANN	Benign	0.84
PhyloP100		0.66
PromoterAI		-0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs881152; hg19: chr5-172198555;