rs10476539

Variant names:

• chr5-92655921-G-A
• rs10476539
• ENST00000512237.1:n.89+985G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000512237.1(ENSG00000249169):​n.89+985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 151,832 control chromosomes in the GnomAD database, including 3,629 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 0.20 (3629 hom., cov: 32)
• Consequence: ENSG00000249169 ENST00000512237.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570
• Publications: 3 publications found

Genes affected

ENSG00000249169 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.291 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000512237.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC105379082	NR_188296.1		n.362+13831C>T		intron	N/A
	LOC105379082	NR_188297.1		n.217+15563C>T		intron	N/A
	LOC105379082	NR_188298.1		n.217+15563C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000249169	ENST00000512237.1	TSL:3	n.89+985G>A		intron	N/A
	ENSG00000249776	ENST00000513779.1	TSL:3	n.134+4809C>T		intron	N/A
	ENSG00000249776	ENST00000718057.1		n.390+13831C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31002 AN: 151714 Hom.: 3620 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.00584

Gnomad SAS AF: 0.0681

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.204 AC: 31031 AN: 151832 Hom.: 3629 Cov.: 32 AF XY: 0.201 AC XY: 14890 AN XY: 74184

African (AFR) AF: 0.296 AC: 12252 AN: 41460

American (AMR) AF: 0.138 AC: 2096 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 594 AN: 3466

East Asian (EAS) AF: 0.00566 AC: 29 AN: 5126

South Asian (SAS) AF: 0.0686 AC: 331 AN: 4828

European-Finnish (FIN) AF: 0.249 AC: 2631 AN: 10562

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12497 AN: 67888

Other (OTH) AF: 0.178 AC: 374 AN: 2106

Alfa AF: 0.186 Hom.: 11898

Bravo AF: 0.203

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.8
DANN	Benign	0.50
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10476539; hg19: chr5-91991628;