5-24775054-T-C

Position:

• chr5-24775054-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.728

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.24775054T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286238	ENST00000651142.1	n.412-783A>G		intron_variant

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

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.0937

Gnomad4 ASJ AF: 0.0952

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.0591

Gnomad4 NFE AF: 0.0647

Gnomad4 OTH AF: 0.179

Alfa AF: 0.104 Hom.: 828

Bravo AF: 0.212

Asia WGS AF: 0.270 AC: 937 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7729215; hg19: chr5-24775163;