chr2-175843077-G-T

Position:

• chr2-175843077-G-T

Variant summary

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

The ENST00000446218.1(EXTL2P1):​n.191G>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 0.672 in 693,154 control chromosomes in the GnomAD database, including 157,576 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 0.70 (37399 hom., cov: 32)
  • Exomes 𝑓: 0.67 (120177 hom.)
• Consequence: EXTL2P1 ENST00000446218.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

Genes affected

EXTL2P1 (HGNC:3517): (exostosin like glycosyltransferase 2 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.791 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
EXTL2P1	ENST00000446218.1	n.191G>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.698 AC: 106073 AN: 151970 Hom.: 37357 Cov.: 32

Gnomad AFR AF: 0.799

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.667

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.685

GnomAD4 exome AF: 0.665 AC: 359958 AN: 541066 Hom.: 120177 Cov.: 7 AF XY: 0.665 AC XY: 194575 AN XY: 292660

Gnomad4 AFR exome AF: 0.791

Gnomad4 AMR exome AF: 0.637

Gnomad4 ASJ exome AF: 0.602

Gnomad4 EAS exome AF: 0.672

Gnomad4 SAS exome AF: 0.668

Gnomad4 FIN exome AF: 0.660

Gnomad4 NFE exome AF: 0.664

Gnomad4 OTH exome AF: 0.678

GnomAD4 genome AF: 0.698 AC: 106170 AN: 152088 Hom.: 37399 Cov.: 32 AF XY: 0.698 AC XY: 51923 AN XY: 74336

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.685

Alfa AF: 0.649 Hom.: 5817

Bravo AF: 0.700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
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: rs6737825; hg19: chr2-176707805;