7-24293991-G-T

Variant names:

• chr7-24293991-G-T
• rs16474
• ENST00000718234.1:n.319+25366C>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+25366C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.504 in 151,912 control chromosomes in the GnomAD database, including 19,685 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 (19685 hom., cov: 32)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.30
• 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=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.65 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+25366C>A		intron	N/A
	ENSG00000228944	ENST00000745512.1		n.341+25366C>A		intron	N/A
	ENSG00000228944	ENST00000745513.1		n.309+25366C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76475 AN: 151794 Hom.: 19675 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.669

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.513

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.504 AC: 76523 AN: 151912 Hom.: 19685 Cov.: 32 AF XY: 0.509 AC XY: 37763 AN XY: 74222

African (AFR) AF: 0.414 AC: 17140 AN: 41418

American (AMR) AF: 0.618 AC: 9433 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1909 AN: 3466

East Asian (EAS) AF: 0.669 AC: 3453 AN: 5164

South Asian (SAS) AF: 0.539 AC: 2601 AN: 4822

European-Finnish (FIN) AF: 0.520 AC: 5471 AN: 10516

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

European-Non Finnish (NFE) AF: 0.513 AC: 34882 AN: 67938

Other (OTH) AF: 0.507 AC: 1072 AN: 2114

Alfa AF: 0.380 Hom.: 1042

Bravo AF: 0.507

Asia WGS AF: 0.564 AC: 1959 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.12
DANN	Benign	0.31
PhyloP100		-3.3

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: rs16474;

hg19: chr7-24333610;