4-89685446-C-T

Variant summary

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

The XR_007058466.1(LOC124900602):n.3942C>T 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 0.687 in 151,994 control chromosomes in the GnomAD database, including 36,316 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 0.69 (36314 hom., cov: 31)
  • Exomes 𝑓: 0.58 (2 hom.)
• Consequence: LOC124900602 XR_007058466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0980

Genes affected

LOC124900602 (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 = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900602	XR_007058466.1	n.3942C>T		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_001741764.2	n.3942C>T		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_007058465.1	n.3942C>T		non_coding_transcript_exon_variant	1/2
LOC124900602	XR_938983.2	n.3942C>T		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659878.1	n.480-40938C>T		intron_variant, non_coding_transcript_variant
	ENST00000673949.1	n.305+16828G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104399 AN: 151864 Hom.: 36303 Cov.: 31

Gnomad AFR AF: 0.705

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.742

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.983

Gnomad SAS AF: 0.784

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.662

GnomAD4 exome AF: 0.583 AC: 7 AN: 12 Hom.: 2 Cov.: 0 AF XY: 0.600 AC XY: 6 AN XY: 10

Gnomad4 NFE exome AF: 0.583

GnomAD4 genome AF: 0.687 AC: 104452 AN: 151982 Hom.: 36314 Cov.: 31 AF XY: 0.691 AC XY: 51316 AN XY: 74246

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.743

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.983

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.640

Gnomad4 OTH AF: 0.665

Alfa AF: 0.628 Hom.: 8973

Bravo AF: 0.692

Asia WGS AF: 0.859 AC: 2984 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	1.7
Dann	Benign	0.62
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs356229; hg19: chr4-90606597;