5-32818967-T-C

Variant names:

• chr5-32818967-T-C
• rs9292468
• ENST00000841800.1:n.496-7872A>G

Variant summary

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

The ENST00000841800.1(ENSG00000250697):​n.496-7872A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,042 control chromosomes in the GnomAD database, including 28,981 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 0.62 (28981 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000841800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 24 publications found

Genes affected

ENSG00000250697 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.654 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
ENSG00000250697	ENST00000841800.1	n.496-7872A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93449 AN: 151924 Hom.: 28939 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.592

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.615 AC: 93546 AN: 152042 Hom.: 28981 Cov.: 32 AF XY: 0.615 AC XY: 45727 AN XY: 74318

African (AFR) AF: 0.661 AC: 27409 AN: 41482

American (AMR) AF: 0.589 AC: 8983 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.592 AC: 2055 AN: 3470

East Asian (EAS) AF: 0.649 AC: 3363 AN: 5178

South Asian (SAS) AF: 0.601 AC: 2891 AN: 4812

European-Finnish (FIN) AF: 0.592 AC: 6250 AN: 10552

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40581 AN: 67972

Other (OTH) AF: 0.620 AC: 1306 AN: 2108

Alfa AF: 0.600 Hom.: 38881

Bravo AF: 0.616

Asia WGS AF: 0.634 AC: 2198 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.085
DANN	Benign	0.42
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs9292468; hg19: chr5-32819073;