1-181855747-T-C

Variant names:

• chr1-181855747-T-C
• rs7533297
• ENST00000717053.1:n.288-20111A>G

Variant summary

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

The ENST00000717053.1(ENSG00000287452):​n.288-20111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.341 in 152,054 control chromosomes in the GnomAD database, including 9,012 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 0.34 (9012 hom., cov: 32)
• Consequence: ENSG00000287452 ENST00000717053.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.518
• Publications: 2 publications found

Genes affected

ENSG00000287452 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.434 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
ENSG00000287452	ENST00000717053.1	n.288-20111A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717054.1	n.293-20111A>G		intron_variant	Intron 1 of 3
ENSG00000287452	ENST00000717055.1	n.81-20111A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51870 AN: 151936 Hom.: 9001 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.381

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.341 AC: 51908 AN: 152054 Hom.: 9012 Cov.: 32 AF XY: 0.341 AC XY: 25375 AN XY: 74314

African (AFR) AF: 0.370 AC: 15336 AN: 41488

American (AMR) AF: 0.382 AC: 5829 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.324 AC: 1123 AN: 3466

East Asian (EAS) AF: 0.449 AC: 2322 AN: 5168

South Asian (SAS) AF: 0.230 AC: 1110 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3596 AN: 10566

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21464 AN: 67956

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.322 Hom.: 13501

Bravo AF: 0.350

Asia WGS AF: 0.344 AC: 1197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs7533297; hg19: chr1-181824882;