7-24294032-A-T

Variant names:

• chr7-24294032-A-T
• rs16473
• ENST00000718234.1:n.319+25325T>A

Variant summary

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

The ENST00000718234.1(ENSG00000228944):​n.319+25325T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 152,004 control chromosomes in the GnomAD database, including 19,513 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 0.50 (19513 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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+25325T>A		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+25325T>A		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+25325T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76168 AN: 151886 Hom.: 19503 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.542

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.508

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

GnomAD4 genome AF: 0.501 AC: 76213 AN: 152004 Hom.: 19513 Cov.: 32 AF XY: 0.506 AC XY: 37571 AN XY: 74288

African (AFR) AF: 0.413 AC: 17129 AN: 41448

American (AMR) AF: 0.617 AC: 9422 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.542 AC: 1881 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3390 AN: 5162

South Asian (SAS) AF: 0.524 AC: 2525 AN: 4820

European-Finnish (FIN) AF: 0.517 AC: 5451 AN: 10548

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.512 AC: 34787 AN: 67960

Other (OTH) AF: 0.505 AC: 1066 AN: 2112

Alfa AF: 0.511 Hom.: 2559

Bravo AF: 0.506

Asia WGS AF: 0.544 AC: 1888 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.46
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs16473; hg19: chr7-24333651;