2-175843077-G-T

Variant names:

• chr2-175843077-G-T
• rs6737825
• ENST00000446218.1:n.191G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000289349 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000446218.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXTL2P1	ENST00000446218.1	TSL:6	n.191G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289349	ENST00000840653.1		n.352+10386G>T		intron	N/A
	ENSG00000289349	ENST00000840654.1		n.498+10386G>T		intron	N/A

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

African (AFR) AF: 0.791 AC: 11673 AN: 14748

American (AMR) AF: 0.637 AC: 19037 AN: 29874

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 8894 AN: 14778

East Asian (EAS) AF: 0.672 AC: 18300 AN: 27212

South Asian (SAS) AF: 0.668 AC: 38905 AN: 58250

European-Finnish (FIN) AF: 0.660 AC: 27362 AN: 41464

Middle Eastern (MID) AF: 0.608 AC: 1645 AN: 2704

European-Non Finnish (NFE) AF: 0.664 AC: 215937 AN: 325170

Other (OTH) AF: 0.678 AC: 18205 AN: 26866

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

African (AFR) AF: 0.798 AC: 33145 AN: 41510

American (AMR) AF: 0.668 AC: 10213 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2131 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3459 AN: 5160

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4820

European-Finnish (FIN) AF: 0.669 AC: 7062 AN: 10562

Middle Eastern (MID) AF: 0.599 AC: 175 AN: 292

European-Non Finnish (NFE) AF: 0.659 AC: 44782 AN: 67960

Other (OTH) AF: 0.685 AC: 1446 AN: 2110

Alfa AF: 0.653 Hom.: 6065

Bravo AF: 0.700

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.67
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6737825; hg19: chr2-176707805;