3-110992334-G-C

Variant names:

• chr3-110992334-G-C
• rs4450855
• ENST00000474769.6:n.241+76930C>G

Variant summary

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

The ENST00000474769.6(NECTIN3-AS1):​n.241+76930C>G variant causes a intron 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: 31)
• Consequence: NECTIN3-AS1 ENST00000474769.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450

Genes affected

NECTIN3-AS1 (HGNC:40813): (NECTIN3 antisense RNA 1)

LOC151760 (HGNC:):

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=-0.93).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC151760	XR_007096272.1	n.483+76930C>G		intron_variant	Intron 2 of 3
LOC151760	XR_007096273.1	n.720+76930C>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000474769.6	n.241+76930C>G		intron_variant	Intron 2 of 3	3
NECTIN3-AS1	ENST00000476301.5	n.502+76930C>G		intron_variant	Intron 2 of 2	4
NECTIN3-AS1	ENST00000485473.2	n.241+76930C>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.4
DANN	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4450855; hg19: chr3-110711181;