chr7-24302506-A-G

Variant names:

• chr7-24302506-A-G
• rs16467
• ENST00000718234.1:n.319+16851T>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+16851T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0421 in 152,346 control chromosomes in the GnomAD database, including 160 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 0.042 (160 hom., cov: 33)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0648 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+16851T>C		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+16851T>C		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+16851T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6409 AN: 152228 Hom.: 160 Cov.: 33

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0254

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0712

Gnomad FIN AF: 0.0228

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0426

Gnomad OTH AF: 0.0430

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

GnomAD4 genome AF: 0.0421 AC: 6413 AN: 152346 Hom.: 160 Cov.: 33 AF XY: 0.0416 AC XY: 3102 AN XY: 74500

African (AFR) AF: 0.0553 AC: 2299 AN: 41582

American (AMR) AF: 0.0254 AC: 389 AN: 15310

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3468

East Asian (EAS) AF: 0.0133 AC: 69 AN: 5192

South Asian (SAS) AF: 0.0710 AC: 343 AN: 4830

European-Finnish (FIN) AF: 0.0228 AC: 242 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0426 AC: 2900 AN: 68018

Other (OTH) AF: 0.0430 AC: 91 AN: 2114

Alfa AF: 0.0478 Hom.: 24

Bravo AF: 0.0417

Asia WGS AF: 0.0560 AC: 195 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		0.029

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: rs16467;

hg19: chr7-24342125;