ENST00000523005.1:n.70-2521G>A

Variant names:

• chr5-172774971-G-A
• rs17658295
• ENST00000523005.1:n.70-2521G>A

Variant summary

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

The ENST00000523005.1(ENSG00000253736):​n.70-2521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,068 control chromosomes in the GnomAD database, including 8,408 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 0.32 (8408 hom., cov: 33)
• Consequence: ENSG00000253736 ENST00000523005.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 10 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377730	NR_188283.1	n.277+2484G>A		intron_variant	Intron 1 of 1
LOC105377730	NR_188284.1	n.277+2484G>A		intron_variant	Intron 1 of 1
LOC105377730	NR_188285.1	n.277+2484G>A		intron_variant	Intron 1 of 2
LOC105377730	NR_188286.1	n.81+1523G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253736	ENST00000523005.1	n.70-2521G>A		intron_variant	Intron 1 of 1	3
ENSG00000253736	ENST00000687811.2	n.287+2484G>A		intron_variant	Intron 1 of 1
ENSG00000289170	ENST00000692849.2	n.90-2171C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48712 AN: 151952 Hom.: 8406 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.320 AC: 48731 AN: 152068 Hom.: 8408 Cov.: 33 AF XY: 0.321 AC XY: 23849 AN XY: 74314

African (AFR) AF: 0.194 AC: 8058 AN: 41490

American (AMR) AF: 0.356 AC: 5440 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.339 AC: 1178 AN: 3472

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5166

South Asian (SAS) AF: 0.296 AC: 1430 AN: 4824

European-Finnish (FIN) AF: 0.392 AC: 4137 AN: 10550

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26083 AN: 67980

Other (OTH) AF: 0.346 AC: 731 AN: 2112

Alfa AF: 0.370 Hom.: 13081

Bravo AF: 0.315

Asia WGS AF: 0.250 AC: 871 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.72
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs17658295; hg19: chr5-172201974; COSMIC: COSV53319845;