5-32814922-A-G

Variant names:

• chr5-32814922-A-G
• rs1173771
• ENST00000841800.1:n.496-3827T>C

Variant summary

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

The ENST00000841800.1(ENSG00000250697):​n.496-3827T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 152,060 control chromosomes in the GnomAD database, including 32,555 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 0.65 (32555 hom., cov: 32)
• Consequence: ENSG00000250697 ENST00000841800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.207
• Publications: 93 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 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.496-3827T>C		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98392 AN: 151942 Hom.: 32502 Cov.: 32

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.596

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.592

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.648 AC: 98502 AN: 152060 Hom.: 32555 Cov.: 32 AF XY: 0.646 AC XY: 47998 AN XY: 74318

African (AFR) AF: 0.774 AC: 32128 AN: 41492

American (AMR) AF: 0.599 AC: 9151 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.596 AC: 2068 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3353 AN: 5160

South Asian (SAS) AF: 0.600 AC: 2885 AN: 4808

European-Finnish (FIN) AF: 0.592 AC: 6249 AN: 10550

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40616 AN: 67994

Other (OTH) AF: 0.635 AC: 1342 AN: 2112

Alfa AF: 0.613 Hom.: 100398

Bravo AF: 0.653

Asia WGS AF: 0.642 AC: 2232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.7
DANN	Benign	0.69
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1173771; hg19: chr5-32815028;