ENST00000746097.1:n.346C>A

Variant names:

• chr7-24283588-G-T
• rs17149106
• ENST00000746097.1:n.346C>A

Variant summary

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

The ENST00000746097.1(ENSG00000297196):​n.346C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0468 in 152,016 control chromosomes in the GnomAD database, including 203 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 0.047 (203 hom., cov: 33)
• Consequence: ENSG00000297196 ENST00000746097.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02
• Publications: 18 publications found

Genes affected

ENSG00000297196 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+35769C>A		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-86559C>A		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+35769C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297196	ENST00000746097.1	n.346C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000297196	ENST00000746098.1	n.401C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000228944	ENST00000718234.1	n.319+35769C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0468 AC: 7116 AN: 151898 Hom.: 203 Cov.: 33

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.0220

Gnomad AMR AF: 0.0270

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.0614

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0388

Gnomad OTH AF: 0.0384

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

GnomAD4 genome AF: 0.0468 AC: 7119 AN: 152016 Hom.: 203 Cov.: 33 AF XY: 0.0481 AC XY: 3571 AN XY: 74314

African (AFR) AF: 0.0686 AC: 2846 AN: 41480

American (AMR) AF: 0.0270 AC: 412 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0133 AC: 46 AN: 3468

East Asian (EAS) AF: 0.0142 AC: 73 AN: 5134

South Asian (SAS) AF: 0.0612 AC: 295 AN: 4820

European-Finnish (FIN) AF: 0.0662 AC: 699 AN: 10558

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0388 AC: 2640 AN: 67966

Other (OTH) AF: 0.0389 AC: 82 AN: 2106

Alfa AF: 0.0254 Hom.: 14

Bravo AF: 0.0440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.37
DANN	Benign	0.56
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs17149106; hg19: chr7-24323207;