rs10507445

Positions:

• chr13-37143095-C-T

Variant summary

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

The ENST00000624379.1(ENSG00000279511):​n.3624G>A 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 0.0245 in 152,276 control chromosomes in the GnomAD database, including 56 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 0.025 (56 hom., cov: 32)
  • Exomes 𝑓: 0.016 (0 hom.)
• Consequence: ENSG00000279511 ENST00000624379.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

Genes affected

ENSG00000279511 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0504 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.37143095C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000279511	ENST00000624379.1	n.3624G>A		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.0245 AC: 3721 AN: 152094 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.0521

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.0184

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0202

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0249

GnomAD4 exome AF: 0.0156 AC: 1 AN: 64 Hom.: 0 Cov.: 0 AF XY: 0.0333 AC XY: 1 AN XY: 30

Gnomad4 FIN exome AF: 0.0167

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.0245 AC: 3735 AN: 152212 Hom.: 56 Cov.: 32 AF XY: 0.0251 AC XY: 1867 AN XY: 74414

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.0145

Gnomad4 ASJ AF: 0.0184

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.00435

Gnomad4 FIN AF: 0.0202

Gnomad4 NFE AF: 0.0142

Gnomad4 OTH AF: 0.0246

Alfa AF: 0.0177 Hom.: 38

Bravo AF: 0.0251

Asia WGS AF: 0.00866 AC: 30 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.25
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10507445; hg19: chr13-37717232;