rs10476539

chr5-92655921-G-A

Variant summary

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

The ENST00000512237.1(ENSG00000249169):n.89+985G>A 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 0.204 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: ENST00000512237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.570

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379082	XR_001742809.2	n.217+15563C>T		intron_variant, non_coding_transcript_variant
LOC105379082	XR_001742810.2	n.397+13831C>T		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948566.3	n.362+13831C>T		intron_variant, non_coding_transcript_variant
LOC105379082	XR_948568.3	n.365+13831C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000512237.1	n.89+985G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000513779.1	n.134+4809C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.00566

Gnomad4 SAS AF: 0.0686

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.184

Gnomad4 OTH AF: 0.178

Alfa AF: 0.182 Hom.: 5368

Bravo AF: 0.203

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.8
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: rs10476539; hg19: chr5-91991628;