rs10520872

Positions:

• chr5-21673871-A-G

Variant summary

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

The ENST00000522350.1(ENSG00000253766):​n.476+49761A>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 0.154 in 152,002 control chromosomes in the GnomAD database, including 1,891 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 (1891 hom., cov: 32)
• Consequence: ENST00000522350.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

Genes affected

(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 = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374685	XR_925848.3	n.3831-2238A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000522350.1	n.476+49761A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23380 AN: 151884 Hom.: 1888 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.154 AC: 23393 AN: 152002 Hom.: 1891 Cov.: 32 AF XY: 0.151 AC XY: 11256 AN XY: 74312

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.173

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.186

Alfa AF: 0.160 Hom.: 1324

Bravo AF: 0.156

Asia WGS AF: 0.184 AC: 634 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10520872; hg19: chr5-21673980;