rs11597812

chr10-5263191-C-G

Variant summary

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

The ENST00000428920.2(ENSG00000231039):n.463C>G 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 0.143 in 152,206 control chromosomes in the GnomAD database, including 2,118 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 0.14 (2117 hom., cov: 32)
  • Exomes 𝑓: 0.20 (1 hom.)
• Consequence: ENST00000428920.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000428920.2	n.463C>G		non_coding_transcript_exon_variant	2/2	3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21676 AN: 152058 Hom.: 2112 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0890

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.0976

Gnomad FIN AF: 0.0599

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0989

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.200 AC: 6 AN: 30 Hom.: 1 Cov.: 0 AF XY: 0.227 AC XY: 5 AN XY: 22

Gnomad4 AFR exome AF: 1.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.200

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.143 AC: 21708 AN: 152176 Hom.: 2117 Cov.: 32 AF XY: 0.137 AC XY: 10181 AN XY: 74400

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.0888

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0215

Gnomad4 SAS AF: 0.0973

Gnomad4 FIN AF: 0.0599

Gnomad4 NFE AF: 0.0989

Gnomad4 OTH AF: 0.140

Alfa AF: 0.125 Hom.: 197

Bravo AF: 0.149

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.2
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11597812; hg19: chr10-5305154;