rs369822

Variant names:

• chr9-17068805-A-G
• rs369822
• ENST00000430545.4:n.393+19764A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000430545.4(ENSG00000237153):​n.393+19764A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 152,046 control chromosomes in the GnomAD database, including 14,825 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 0.44 (14825 hom., cov: 32)
• Consequence: ENSG00000237153 ENST00000430545.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

ENSG00000237153 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.488 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
ENSG00000237153	ENST00000430545.4	n.393+19764A>G		intron_variant	Intron 2 of 2	5
ENSG00000237153	ENST00000649821.1	n.179+15805A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66171 AN: 151928 Hom.: 14798 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.436 AC: 66243 AN: 152046 Hom.: 14825 Cov.: 32 AF XY: 0.421 AC XY: 31269 AN XY: 74346

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.442

Alfa AF: 0.446 Hom.: 2526

Bravo AF: 0.447

Asia WGS AF: 0.294 AC: 1022 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	1.7
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs369822; hg19: chr9-17068803;