chr2-1554155-T-C

Position:

• chr2-1554155-T-C

Variant summary

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

The NR_168373.1(LOC102723730):​n.746-15T>C variant causes a splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,044 control chromosomes in the GnomAD database, including 6,256 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 0.27 (6256 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: LOC102723730 NR_168373.1 splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723730	NR_168373.1	n.746-15T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000438247.1	n.516-7220A>G		intron_variant, non_coding_transcript_variant		4
	ENST00000640435.1	n.231-15T>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		5
	ENST00000650512.1	n.547+26046A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40670 AN: 151926 Hom.: 6231 Cov.: 33

Gnomad AFR AF: 0.427

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.230

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.268 AC: 40760 AN: 152044 Hom.: 6256 Cov.: 33 AF XY: 0.268 AC XY: 19949 AN XY: 74318

Gnomad4 AFR AF: 0.427

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.236

Alfa AF: 0.256 Hom.: 892

Bravo AF: 0.272

Asia WGS AF: 0.273 AC: 948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.6
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10206020; hg19: chr2-1557927;