rs11249215

Positions:

• chr1-24970693-G-A

Variant summary

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

The ENST00000568143.1(ENSG00000261025):​n.173C>T 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 0.445 in 154,256 control chromosomes in the GnomAD database, including 16,262 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 0.44 (15999 hom., cov: 31)
  • Exomes 𝑓: 0.47 (263 hom.)
• Consequence: ENST00000568143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000568143.1	n.173C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67397 AN: 151724 Hom.: 15969 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.477

GnomAD4 exome AF: 0.466 AC: 1124 AN: 2414 Hom.: 263 Cov.: 0 AF XY: 0.466 AC XY: 569 AN XY: 1220

Gnomad4 AFR exome AF: 0.259

Gnomad4 AMR exome AF: 0.625

Gnomad4 ASJ exome AF: 0.412

Gnomad4 EAS exome AF: 0.463

Gnomad4 SAS exome AF: 0.722

Gnomad4 FIN exome AF: 0.561

Gnomad4 NFE exome AF: 0.455

Gnomad4 OTH exome AF: 0.440

GnomAD4 genome AF: 0.444 AC: 67450 AN: 151842 Hom.: 15999 Cov.: 31 AF XY: 0.458 AC XY: 33982 AN XY: 74224

Gnomad4 AFR AF: 0.275

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.539

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.559

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.483

Alfa AF: 0.477 Hom.: 33422

Bravo AF: 0.434

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11249215; hg19: chr1-25297184;