7-24294450-A-G

Variant names:

• chr7-24294450-A-G
• rs16472
• ENST00000718234.1:n.319+24907T>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+24907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.924 in 152,290 control chromosomes in the GnomAD database, including 65,120 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 0.92 (65120 hom., cov: 33)
• Consequence: ENSG00000228944 ENST00000718234.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20
• 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986777	XR_001745121.2	n.209+24907T>C		intron_variant	Intron 2 of 2
LOC107986777	XR_001745122.2	n.81-97421T>C		intron_variant	Intron 1 of 1
LOC107986777	XR_001745123.2	n.209+24907T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228944	ENST00000718234.1	n.319+24907T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745512.1	n.341+24907T>C		intron_variant	Intron 2 of 5
ENSG00000228944	ENST00000745513.1	n.309+24907T>C		intron_variant	Intron 2 of 3
ENSG00000228944	ENST00000745514.1	n.329-24620T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.924 AC: 140675 AN: 152172 Hom.: 65069 Cov.: 33

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.985

Gnomad SAS AF: 0.926

Gnomad FIN AF: 0.882

Gnomad MID AF: 0.955

Gnomad NFE AF: 0.916

Gnomad OTH AF: 0.934

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

GnomAD4 genome AF: 0.924 AC: 140783 AN: 152290 Hom.: 65120 Cov.: 33 AF XY: 0.924 AC XY: 68827 AN XY: 74454

African (AFR) AF: 0.928 AC: 38565 AN: 41562

American (AMR) AF: 0.949 AC: 14512 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3318 AN: 3470

East Asian (EAS) AF: 0.985 AC: 5110 AN: 5186

South Asian (SAS) AF: 0.927 AC: 4470 AN: 4824

European-Finnish (FIN) AF: 0.882 AC: 9338 AN: 10592

Middle Eastern (MID) AF: 0.962 AC: 281 AN: 292

European-Non Finnish (NFE) AF: 0.916 AC: 62351 AN: 68040

Other (OTH) AF: 0.929 AC: 1964 AN: 2114

Alfa AF: 0.922 Hom.: 124282

Bravo AF: 0.931

Asia WGS AF: 0.932 AC: 3243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	8.5
DANN	Benign	0.47
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs16472; hg19: chr7-24334069;