ENST00000822409.1:n.379+8444G>A

Variant names:

• chr13-45326132-G-A
• rs7323755
• ENST00000822409.1:n.379+8444G>A

Variant summary

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

The ENST00000822409.1(ENSG00000273149):​n.379+8444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0591 in 152,262 control chromosomes in the GnomAD database, including 404 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 0.059 (404 hom., cov: 31)
• Consequence: ENSG00000273149 ENST00000822409.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 12 publications found

Genes affected

ENSG00000273149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.115 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
ENSG00000273149	ENST00000822409.1	n.379+8444G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0589 AC: 8966 AN: 152144 Hom.: 400 Cov.: 31

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0309

Gnomad ASJ AF: 0.0501

Gnomad EAS AF: 0.0785

Gnomad SAS AF: 0.0788

Gnomad FIN AF: 0.0327

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0322

Gnomad OTH AF: 0.0535

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

GnomAD4 genome AF: 0.0591 AC: 8995 AN: 152262 Hom.: 404 Cov.: 31 AF XY: 0.0594 AC XY: 4426 AN XY: 74458

African (AFR) AF: 0.118 AC: 4889 AN: 41532

American (AMR) AF: 0.0308 AC: 471 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0501 AC: 174 AN: 3472

East Asian (EAS) AF: 0.0785 AC: 407 AN: 5188

South Asian (SAS) AF: 0.0784 AC: 378 AN: 4820

European-Finnish (FIN) AF: 0.0327 AC: 347 AN: 10616

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0322 AC: 2192 AN: 68016

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0444 Hom.: 742

Bravo AF: 0.0610

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs7323755; hg19: chr13-45900267;