rs327837

chr5-125829498-G-A

Variant summary

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

The ENST00000651847.1(ENSG00000248752):n.594-1492C>T 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 0.345 in 152,014 control chromosomes in the GnomAD database, including 9,407 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 0.35 (9407 hom., cov: 32)
• Consequence: ENST00000651847.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901056	XR_007058919.1	n.1775-1492C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651847.1	n.594-1492C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52479 AN: 151894 Hom.: 9409 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.345 AC: 52493 AN: 152014 Hom.: 9407 Cov.: 32 AF XY: 0.343 AC XY: 25492 AN XY: 74282

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.362

Alfa AF: 0.377 Hom.: 2190

Bravo AF: 0.341

Asia WGS AF: 0.325 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs327837; hg19: chr5-125165191; COSMIC: COSV60195100;