rs11249215

Variant names:

• chr1-24970693-G-A
• rs11249215
• ENST00000568143.1:n.173C>T

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: ENSG00000261025 ENST00000568143.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

ENSG00000261025 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000261025	ENST00000568143.1	n.173C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;