7-24292516-A-G

Variant names:

• chr7-24292516-A-G
• rs16123
• ENST00000718234.1:n.319+26841T>C

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+26841T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0716 in 152,192 control chromosomes in the GnomAD database, including 782 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 0.072 (782 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116
• Publications: 5 publications found

Genes affected

ENSG00000228944 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.276 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718234.1. 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
	ENSG00000228944	ENST00000718234.1		n.319+26841T>C		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+26841T>C		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+26841T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0714 AC: 10865 AN: 152074 Hom.: 782 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0309

Gnomad OTH AF: 0.0731

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

GnomAD4 genome AF: 0.0716 AC: 10891 AN: 152192 Hom.: 782 Cov.: 32 AF XY: 0.0791 AC XY: 5885 AN XY: 74408

African (AFR) AF: 0.0650 AC: 2700 AN: 41540

American (AMR) AF: 0.182 AC: 2776 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0660 AC: 229 AN: 3472

East Asian (EAS) AF: 0.288 AC: 1486 AN: 5156

South Asian (SAS) AF: 0.180 AC: 866 AN: 4824

European-Finnish (FIN) AF: 0.0529 AC: 561 AN: 10598

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0309 AC: 2100 AN: 68004

Other (OTH) AF: 0.0747 AC: 158 AN: 2114

Alfa AF: 0.0478 Hom.: 1503

Bravo AF: 0.0793

Asia WGS AF: 0.243 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.85
PhyloP100		0.12

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: rs16123;

hg19: chr7-24332135;