chr5-124496959-C-T

Position:

• chr5-124496959-C-T

Variant summary

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

The ENST00000503145.1(ENSG00000248296):​n.387-3774G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.259 in 151,956 control chromosomes in the GnomAD database, including 6,490 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 0.26 (6490 hom., cov: 31)
• Consequence: ENST00000503145.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.436

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503145.1	n.387-3774G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39283 AN: 151838 Hom.: 6470 Cov.: 31

Gnomad AFR AF: 0.0836

Gnomad AMI AF: 0.275

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.618

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.259 AC: 39337 AN: 151956 Hom.: 6490 Cov.: 31 AF XY: 0.274 AC XY: 20342 AN XY: 74242

Gnomad4 AFR AF: 0.0839

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.242

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.463

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.263

Alfa AF: 0.257 Hom.: 866

Bravo AF: 0.246

Asia WGS AF: 0.532 AC: 1849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12513663; hg19: chr5-123832652;