rs3007456

Variant names:

• chr9-42295738-T-A
• rs3007456
• ENST00000840058.1:n.466T>A

Your query was ambiguous. Multiple possible variants found:

• chr9-42295738-T-A
• chr9-42295738-T-C
• chr9-42295738-T-G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000840058.1(ENSG00000275649):​n.466T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.0 (0 hom., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000275649 ENST00000840058.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 1 publications found

Genes affected

ENSG00000275649 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

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
ENSG00000275649	ENST00000840058.1	n.466T>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000275649	ENST00000614030.1	n.27-28168T>A		intron_variant	Intron 1 of 3	5
ENSG00000275649	ENST00000840056.1	n.400-28168T>A		intron_variant	Intron 1 of 3
ENSG00000275649	ENST00000840057.1	n.364-28168T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 0 AN: 133484 Hom.: 0 Cov.: 23

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 133484 Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0 AN XY: 64686

African (AFR) AF: 0.00 AC: 0 AN: 34132

American (AMR) AF: 0.00 AC: 0 AN: 13258

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3160

East Asian (EAS) AF: 0.00 AC: 0 AN: 4364

South Asian (SAS) AF: 0.00 AC: 0 AN: 4122

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9218

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 302

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 62282

Other (OTH) AF: 0.00 AC: 0 AN: 1790

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.1
DANN	Benign	0.29
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs3007456; hg19: chr9-43518651;