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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746097.1. 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
	ENSG00000297196	ENST00000746097.1		n.346C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297196	ENST00000746098.1		n.401C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228944	ENST00000718234.1		n.319+35769C>A		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17149106;

hg19: chr7-24323207;