7-24283791-T-C

Variant names:

• chr7-24283791-T-C
• rs16147
• ENST00000746097.1:n.143A>G

Variant summary

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

The ENST00000746097.1(ENSG00000297196):​n.143A>G 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 0.49 in 152,122 control chromosomes in the GnomAD database, including 18,859 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 0.49 (18859 hom., cov: 33)
• Consequence: ENSG00000297196 ENST00000746097.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 161 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.644 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.143A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000297196	ENST00000746098.1		n.198A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000228944	ENST00000718234.1		n.319+35566A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74449 AN: 152004 Hom.: 18851 Cov.: 33

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.490 AC: 74486 AN: 152122 Hom.: 18859 Cov.: 33 AF XY: 0.494 AC XY: 36745 AN XY: 74370

African (AFR) AF: 0.373 AC: 15494 AN: 41520

American (AMR) AF: 0.608 AC: 9303 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1921 AN: 3472

East Asian (EAS) AF: 0.663 AC: 3430 AN: 5174

South Asian (SAS) AF: 0.528 AC: 2547 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5453 AN: 10570

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34741 AN: 67956

Other (OTH) AF: 0.497 AC: 1049 AN: 2110

Alfa AF: 0.504 Hom.: 47265

Bravo AF: 0.492

Asia WGS AF: 0.546 AC: 1900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.64
PhyloP100		-0.17
PromoterAI		-0.0066	Neutral

Splicing

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

Other links and lift over

dbSNP: rs16147; hg19: chr7-24323410;