rs3025365

Positions:

• chr9-133617354-A-G

Variant summary

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

The ENST00000564021.1(ENSG00000261018):​n.114-3680T>C 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 0.202 in 151,942 control chromosomes in the GnomAD database, including 3,766 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 0.20 (3766 hom., cov: 32)
• Consequence: ENST00000564021.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.33 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000564021.1	n.114-3680T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30623 AN: 151824 Hom.: 3754 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.163

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.202 AC: 30675 AN: 151942 Hom.: 3766 Cov.: 32 AF XY: 0.202 AC XY: 15032 AN XY: 74268

Gnomad4 AFR AF: 0.335

Gnomad4 AMR AF: 0.163

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.155

Alfa AF: 0.150 Hom.: 2552

Bravo AF: 0.205

Asia WGS AF: 0.207 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.082
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3025365; hg19: chr9-136482476;