rs6558073

Variant names:

• chr8-28756010-G-A
• rs6558073
• NM_001437797.1:c.*5144G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-28756010-G-A
• chr8-28756010-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001437797.1(EXTL3):​c.*5144G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: EXTL3 NM_001437797.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738
• Publications: 3 publications found

Genes affected

EXTL3 (HGNC:3518): (exostosin like glycosyltransferase 3) This gene encodes a single-pass membrane protein which functions as a glycosyltransferase. The encoded protein catalyzes the transfer of N-acetylglucosamine to glycosaminoglycan chains. This reaction is important in heparin and heparan sulfate synthesis. Alternative splicing results in the multiple transcript variants. [provided by RefSeq, Nov 2012]

EXTL3 Gene-Disease associations (from GenCC):

• immunoskeletal dysplasia with neurodevelopmental abnormalities

  Inheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001437797.1. 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
	EXTL3	NM_001437797.1		c.*5144G>A		3_prime_UTR	Exon 6 of 6	NP_001424726.1	A0A384NPY9
	EXTL3	NM_001438399.1		c.*5144G>A		3_prime_UTR	Exon 7 of 7	NP_001425328.1
	EXTL3	NM_001438400.1		c.*5144G>A		3_prime_UTR	Exon 8 of 8	NP_001425329.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EXTL3	ENST00000696177.1		c.*5144G>A		3_prime_UTR	Exon 6 of 6	ENSP00000512467.1	O43909
	EXTL3	ENST00000696178.1		c.*5144G>A		3_prime_UTR	Exon 7 of 7	ENSP00000512468.1	O43909
	EXTL3	ENST00000696182.1		c.*5144G>A		3_prime_UTR	Exon 5 of 5	ENSP00000512472.1	A0A8Q3SIK7

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.25
DANN	Benign	0.89
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs6558073; hg19: chr8-28613527;