rs9634328

Variant names:

• chr13-21664407-A-C
• rs9634328
• ENST00000701135.2:n.277+6190T>G

Variant summary

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

The ENST00000701135.2(ENSG00000289860):​n.277+6190T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,074 control chromosomes in the GnomAD database, including 7,269 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 0.30 (7269 hom., cov: 32)
• Consequence: ENSG00000289860 ENST00000701135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.379
• Publications: 5 publications found

Genes affected

ENSG00000289860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.55).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701135.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289860	ENST00000701135.2		n.277+6190T>G		intron	N/A
	ENSG00000289860	ENST00000753720.1		n.310+6190T>G		intron	N/A
	ENSG00000289860	ENST00000753721.1		n.352+6190T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45754 AN: 151956 Hom.: 7264 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.301 AC: 45778 AN: 152074 Hom.: 7269 Cov.: 32 AF XY: 0.301 AC XY: 22404 AN XY: 74354

African (AFR) AF: 0.217 AC: 8987 AN: 41504

American (AMR) AF: 0.241 AC: 3677 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 834 AN: 3462

East Asian (EAS) AF: 0.508 AC: 2616 AN: 5154

South Asian (SAS) AF: 0.396 AC: 1907 AN: 4814

European-Finnish (FIN) AF: 0.351 AC: 3708 AN: 10578

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23064 AN: 67974

Other (OTH) AF: 0.281 AC: 593 AN: 2112

Alfa AF: 0.325 Hom.: 6596

Bravo AF: 0.290

Asia WGS AF: 0.458 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.55
CADD	Benign	6.2
DANN	Benign	0.88
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9634328; hg19: chr13-22238546;