rs9332456

Variant names:

• chr5-1993901-C-T
• rs9332456
• ENST00000653000.1:n.665+44640C>T

Variant summary

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

The ENST00000653000.1(ENSG00000248994):​n.665+44640C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,104 control chromosomes in the GnomAD database, including 16,848 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 0.46 (16848 hom., cov: 33)
• Consequence: ENSG00000248994 ENST00000653000.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 2 publications found

Genes affected

ENSG00000248994 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374618	NR_171679.1	n.534+59916C>T		intron_variant	Intron 2 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248994	ENST00000653000.1	n.665+44640C>T		intron_variant	Intron 2 of 8
ENSG00000248994	ENST00000745995.1	n.395+59916C>T		intron_variant	Intron 2 of 2
ENSG00000248994	ENST00000745996.1	n.318+44640C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70645 AN: 151986 Hom.: 16844 Cov.: 33

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.496

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.463

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

GnomAD4 genome AF: 0.465 AC: 70695 AN: 152104 Hom.: 16848 Cov.: 33 AF XY: 0.460 AC XY: 34200 AN XY: 74338

African (AFR) AF: 0.387 AC: 16077 AN: 41498

American (AMR) AF: 0.496 AC: 7573 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.376 AC: 1305 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1650 AN: 5178

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4826

European-Finnish (FIN) AF: 0.480 AC: 5068 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35733 AN: 67978

Other (OTH) AF: 0.458 AC: 966 AN: 2108

Alfa AF: 0.492 Hom.: 2432

Bravo AF: 0.463

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.32
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs9332456; hg19: chr5-1994015;