5-151383977-C-T

Position:

• chr5-151383977-C-T

Variant summary

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

The ENST00000517788.1(ENSG00000253897):​n.950+3086G>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 0.294 in 151,748 control chromosomes in the GnomAD database, including 7,911 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 0.29 (7911 hom., cov: 31)
• Consequence: ENST00000517788.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.65

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378234	XR_007059006.1	n.1208+28555G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000517788.1	n.950+3086G>A		intron_variant, non_coding_transcript_variant
	ENST00000647906.1	n.1057-17319G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44558 AN: 151630 Hom.: 7897 Cov.: 31

Gnomad AFR AF: 0.492

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.294 AC: 44610 AN: 151748 Hom.: 7911 Cov.: 31 AF XY: 0.289 AC XY: 21406 AN XY: 74094

Gnomad4 AFR AF: 0.492

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.0151

Gnomad4 SAS AF: 0.137

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.239

Gnomad4 OTH AF: 0.262

Alfa AF: 0.288 Hom.: 862

Bravo AF: 0.295

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.15
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285645; hg19: chr5-150763538; COSMIC: COSV72957606;