5-172766871-A-G

Variant names:

• chr5-172766871-A-G
• rs178723
• ENST00000523005.1:n.69+3823A>G

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.69+3823A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.481 in 152,170 control chromosomes in the GnomAD database, including 17,873 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 0.48 (17873 hom., cov: 33)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

ENSG00000253736 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 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.69+3823A>G		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.481 AC: 73106 AN: 152052 Hom.: 17859 Cov.: 33

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.553

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.481 AC: 73162 AN: 152170 Hom.: 17873 Cov.: 33 AF XY: 0.483 AC XY: 35902 AN XY: 74372

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.519

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.553

Gnomad4 SAS AF: 0.520

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.507

Alfa AF: 0.501 Hom.: 7060

Bravo AF: 0.481

Asia WGS AF: 0.514 AC: 1788 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	2.4
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs178723; hg19: chr5-172193874;