rs10516842

chr4-89685029-A-G

Variant summary

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

The XR_007058466.1(LOC124900602):n.3525A>G 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 0.0556 in 152,162 control chromosomes in the GnomAD database, including 447 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 0.056 (447 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: LOC124900602 XR_007058466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

Genes affected

LOC124900602 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124900602	XR_007058466.1	n.3525A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_001741764.2	n.3525A>G		non_coding_transcript_exon_variant	1/3
LOC124900602	XR_007058465.1	n.3525A>G		non_coding_transcript_exon_variant	1/2
LOC124900602	XR_938983.2	n.3525A>G		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000659878.1	n.480-41355A>G		intron_variant, non_coding_transcript_variant
	ENST00000673949.1	n.305+17245T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0554 AC: 8423 AN: 152046 Hom.: 438 Cov.: 32

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0259

Gnomad ASJ AF: 0.00231

Gnomad EAS AF: 0.0574

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0528

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0223

Gnomad OTH AF: 0.0416

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0556 AC: 8463 AN: 152162 Hom.: 447 Cov.: 32 AF XY: 0.0556 AC XY: 4138 AN XY: 74408

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.0258

Gnomad4 ASJ AF: 0.00231

Gnomad4 EAS AF: 0.0578

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.0528

Gnomad4 NFE AF: 0.0223

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0415 Hom.: 42

Bravo AF: 0.0577

Asia WGS AF: 0.0700 AC: 243 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.7
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: rs10516842; hg19: chr4-90606180;