5-32888712-C-T

Variant summary

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

The XR_007058723.1(LOC124900955):n.346G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 151,922 control chromosomes in the GnomAD database, including 13,365 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 0.41 (13365 hom., cov: 32)
• Consequence: LOC124900955 XR_007058723.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

LOC124900955 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900955	XR_007058723.1	n.346G>A		non_coding_transcript_exon_variant	4/4
LOC124900956	XR_007058724.1	n.5729-1041C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666525.1	n.674G>A		non_coding_transcript_exon_variant	5/5

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61780 AN: 151804 Hom.: 13358 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.407 AC: 61803 AN: 151922 Hom.: 13365 Cov.: 32 AF XY: 0.408 AC XY: 30286 AN XY: 74242

Gnomad4 AFR AF: 0.260

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.370

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.518

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.457

Gnomad4 OTH AF: 0.406

Alfa AF: 0.455 Hom.: 34661

Bravo AF: 0.409

Asia WGS AF: 0.509 AC: 1770 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.48
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10472828; hg19: chr5-32888818;