rs10052709

Positions:

• chr5-159333469-C-G

Variant summary

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

The NR_037889.1(LOC285626):​n.745+466C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,084 control chromosomes in the GnomAD database, including 1,737 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 0.15 (1737 hom., cov: 32)
• Consequence: LOC285626 NR_037889.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.904

Genes affected

LOC285626 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC285626	NR_037889.1	n.745+466C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000515337.1	n.745+466C>G		intron_variant, non_coding_transcript_variant		2
	ENST00000641150.1	n.324+466C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22055 AN: 151966 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0989

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.0765

Gnomad SAS AF: 0.0547

Gnomad FIN AF: 0.0770

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.136

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.145 AC: 22053 AN: 152084 Hom.: 1737 Cov.: 32 AF XY: 0.139 AC XY: 10321 AN XY: 74348

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.0761

Gnomad4 SAS AF: 0.0541

Gnomad4 FIN AF: 0.0770

Gnomad4 NFE AF: 0.136

Gnomad4 OTH AF: 0.152

Alfa AF: 0.143 Hom.: 226

Bravo AF: 0.153

Asia WGS AF: 0.0680 AC: 236 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.31
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10052709; hg19: chr5-158760477;