rs369822

Positions:

• chr9-17068805-A-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, non coding transcript 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: ENST00000430545.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000430545.4	n.393+19764A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000649821.1	n.179+15805A>G		intron_variant, non_coding_transcript_variant

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;