rs2285044

Variant names:

• chr3-50299230-T-A
• rs2285044
• NM_003549.4:c.-35A>T

Your query was ambiguous. Multiple possible variants found:

• chr3-50299230-T-A
• chr3-50299230-T-C
• chr3-50299230-T-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003549.4(HYAL3):​c.-35A>T variant causes a 5 prime UTR premature start codon gain 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: 33)
• Consequence: HYAL3 NM_003549.4 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

HYAL3 (HGNC:5322): (hyaluronidase 3) This gene encodes a member of the hyaluronidase family. Hyaluronidases are endoglycosidase enzymes that degrade hyaluronan, one of the major glycosaminoglycans of the extracellular matrix. The regulated turnover of hyaluronan plays a critical role in many biological processes including cell proliferation, migration and differentiation. The encoded protein may also play an important role in sperm function. This gene is one of several related genes in a region of chromosome 3p21.3 associated with tumor suppression, and the expression of specific transcript variants may be indicative of tumor status. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and some isoforms may lack hyaluronidase activity. This gene overlaps and is on the same strand as N-acetyltransferase 6 (GCN5-related), and some transcripts of each gene share a portion of the first exon. [provided by RefSeq, Jan 2011]

NAA80 (HGNC:30252): (N-alpha-acetyltransferase 80, NatH catalytic subunit) This gene encodes a member of the N-acetyltransferase family. N-acetyltransferases modify proteins by transferring acetyl groups from acetyl CoA to the N-termini of protein substrates. The encoded protein is a cytoplasmic N-acetyltransferase with a substrate specificity for proteins with an N-terminal methionine. This gene is located in the tumor suppressor gene region on chromosome 3p21.3 and the encoded protein may play a role in cancer. Alternatively spliced transcript variants encoding multiple isoforms have been observed. This gene overlaps and is on the same strand as hyaluronoglucosaminidase 3, and some transcripts of each gene share a portion of the first exon. [provided by RefSeq, Jan 2011]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HYAL3	NM_003549.4	c.-35A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 4	ENST00000336307.6	NP_003540.2
NAA80	NM_001200016.2	c.-227A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 2	ENST00000443094.3	NP_001186945.1
HYAL3	NM_003549.4	c.-35A>T		5_prime_UTR_variant	Exon 1 of 4	ENST00000336307.6	NP_003540.2
NAA80	NM_001200016.2	c.-227A>T		5_prime_UTR_variant	Exon 1 of 2	ENST00000443094.3	NP_001186945.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HYAL3	ENST00000336307.6	c.-35A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 4	1	NM_003549.4	ENSP00000337425.1
NAA80	ENST00000443094.3	c.-227A>T		5_prime_UTR_premature_start_codon_gain_variant	Exon 1 of 2	1	NM_001200016.2	ENSP00000410610.2
HYAL3	ENST00000336307.6	c.-35A>T		5_prime_UTR_variant	Exon 1 of 4	1	NM_003549.4	ENSP00000337425.1
NAA80	ENST00000443094.3	c.-227A>T		5_prime_UTR_variant	Exon 1 of 2	1	NM_001200016.2	ENSP00000410610.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	7.3
DANN	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2285044; hg19: chr3-50336661;