rs6737825

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-175843077-G-A
• chr2-175843077-G-C
• chr2-175843077-G-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000446218.1(EXTL2P1):​n.191G>A 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 0.000157 in 694,354 control chromosomes in the GnomAD database, including 1 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 0.00049 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000065 (1 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

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>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289349	ENST00000840653.1		n.352+10386G>A		intron	N/A
	ENSG00000289349	ENST00000840654.1		n.498+10386G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.000434 AC: 66 AN: 152034 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00157

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000655

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.0000646 AC: 35 AN: 542202 Hom.: 1 Cov.: 7 AF XY: 0.0000682 AC XY: 20 AN XY: 293224

African (AFR) AF: 0.00135 AC: 20 AN: 14778

American (AMR) AF: 0.00 AC: 0 AN: 29978

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 14816

East Asian (EAS) AF: 0.00 AC: 0 AN: 27260

South Asian (SAS) AF: 0.00 AC: 0 AN: 58350

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41528

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2718

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 325860

Other (OTH) AF: 0.000557 AC: 15 AN: 26914

GnomAD4 genome AF: 0.000486 AC: 74 AN: 152152 Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40 AN XY: 74380

African (AFR) AF: 0.00176 AC: 73 AN: 41522

American (AMR) AF: 0.0000654 AC: 1 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5166

South Asian (SAS) AF: 0.00 AC: 0 AN: 4822

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10578

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67984

Other (OTH) AF: 0.00 AC: 0 AN: 2112

Alfa AF: 0.00 Hom.: 6065

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.95
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;