rs10516264

Positions:

• chr4-13032521-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The XR_007058050.1(LOC124900668):​n.16766G>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 0.021 in 152,256 control chromosomes in the GnomAD database, including 49 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 0.021 (49 hom., cov: 32)
• Consequence: LOC124900668 XR_007058050.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900

Genes affected

LOC124900668 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.021 (3190/152256) while in subpopulation AFR AF= 0.0355 (1473/41544). AF 95% confidence interval is 0.0339. There are 49 homozygotes in gnomad4. There are 1573 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 49 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900668	XR_007058050.1	n.16766G>A		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0209 AC: 3181 AN: 152138 Hom.: 48 Cov.: 32

Gnomad AFR AF: 0.0353

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.00897

Gnomad ASJ AF: 0.0159

Gnomad EAS AF: 0.00732

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.0195

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0157

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0210 AC: 3190 AN: 152256 Hom.: 49 Cov.: 32 AF XY: 0.0211 AC XY: 1573 AN XY: 74460

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.00896

Gnomad4 ASJ AF: 0.0159

Gnomad4 EAS AF: 0.00734

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.0195

Gnomad4 NFE AF: 0.0157

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0188 Hom.: 6

Bravo AF: 0.0213

Asia WGS AF: 0.0140 AC: 49 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	3.3
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516264; hg19: chr4-13034145;