rs11249215

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 39 publications found

Genes affected

ENSG00000261025 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000568143.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261025	ENST00000568143.1	TSL:6	n.173C>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000261025	ENST00000751467.1		n.330+584C>T		intron	N/A

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

African (AFR) AF: 0.259 AC: 14 AN: 54

American (AMR) AF: 0.625 AC: 25 AN: 40

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 28 AN: 68

East Asian (EAS) AF: 0.463 AC: 151 AN: 326

South Asian (SAS) AF: 0.722 AC: 13 AN: 18

European-Finnish (FIN) AF: 0.561 AC: 147 AN: 262

Middle Eastern (MID) AF: 0.333 AC: 2 AN: 6

European-Non Finnish (NFE) AF: 0.455 AC: 693 AN: 1524

Other (OTH) AF: 0.440 AC: 51 AN: 116

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

African (AFR) AF: 0.275 AC: 11371 AN: 41388

American (AMR) AF: 0.561 AC: 8574 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.468 AC: 1623 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2781 AN: 5156

South Asian (SAS) AF: 0.626 AC: 3011 AN: 4812

European-Finnish (FIN) AF: 0.559 AC: 5904 AN: 10564

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.477 AC: 32399 AN: 67864

Other (OTH) AF: 0.483 AC: 1017 AN: 2106

Alfa AF: 0.466 Hom.: 69464

Bravo AF: 0.434

Asia WGS AF: 0.596 AC: 2071 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.6
DANN	Benign	0.75
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs11249215; hg19: chr1-25297184;