rs10516264

Variant names:

• chr4-13032521-C-T
• rs10516264
• XR_007058050.1:n.16766G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

LOC124900668 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900668	XR_007058050.1	n.16766G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0355 AC: 1473 AN: 41544

American (AMR) AF: 0.00896 AC: 137 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0159 AC: 55 AN: 3470

East Asian (EAS) AF: 0.00734 AC: 38 AN: 5180

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4822

European-Finnish (FIN) AF: 0.0195 AC: 207 AN: 10610

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0157 AC: 1068 AN: 68016

Other (OTH) AF: 0.0227 AC: 48 AN: 2114

Alfa AF: 0.0190 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
PhyloP100		0.090

Splicing

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

Other links and lift over

dbSNP: rs10516264; hg19: chr4-13034145;