5-24775054-T-C

Variant names:

• chr5-24775054-T-C
• rs7729215
• ENST00000651142.1:n.412-783A>G

Variant summary

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

The ENST00000651142.1(ENSG00000286238):​n.412-783A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 151,694 control chromosomes in the GnomAD database, including 5,922 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 0.20 (5922 hom., cov: 32)
• Consequence: ENSG00000286238 ENST00000651142.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728
• Publications: 1 publications found

Genes affected

ENSG00000286238 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651142.1. 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
	ENSG00000286238	ENST00000651142.1		n.412-783A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30077 AN: 151574 Hom.: 5903 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0952

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.0591

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0646

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.199 AC: 30148 AN: 151694 Hom.: 5922 Cov.: 32 AF XY: 0.196 AC XY: 14517 AN XY: 74116

African (AFR) AF: 0.508 AC: 20979 AN: 41322

American (AMR) AF: 0.0937 AC: 1427 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.0952 AC: 330 AN: 3466

East Asian (EAS) AF: 0.172 AC: 885 AN: 5148

South Asian (SAS) AF: 0.225 AC: 1076 AN: 4776

European-Finnish (FIN) AF: 0.0591 AC: 624 AN: 10562

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.0647 AC: 4389 AN: 67884

Other (OTH) AF: 0.179 AC: 377 AN: 2104

Alfa AF: 0.105 Hom.: 972

Bravo AF: 0.212

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.26
DANN	Benign	0.26
PhyloP100		-0.73

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: rs7729215;

hg19: chr5-24775163;