rs1462795

chr3-110973907-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000485473.2(NECTIN3-AS1):n.242-80077A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.709 in 152,062 control chromosomes in the GnomAD database, including 43,874 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 0.71 (43874 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000485473.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.615

Genes affected

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

LOC151760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.921 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC151760	XR_007096272.1	n.484-80077A>G		intron_variant, non_coding_transcript_variant
LOC151760	XR_007096273.1	n.721-80077A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NECTIN3-AS1	ENST00000485473.2	n.242-80077A>G		intron_variant, non_coding_transcript_variant		3
NECTIN3-AS1	ENST00000474769.6	n.242-80077A>G		intron_variant, non_coding_transcript_variant		3
NECTIN3-AS1	ENST00000476301.5	n.503-80077A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107863 AN: 151946 Hom.: 43876 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.857

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.881

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.791

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.741

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

GnomAD4 genome AF: 0.709 AC: 107880 AN: 152062 Hom.: 43874 Cov.: 32 AF XY: 0.706 AC XY: 52525 AN XY: 74346

Gnomad4 AFR AF: 0.298

Gnomad4 AMR AF: 0.749

Gnomad4 ASJ AF: 0.881

Gnomad4 EAS AF: 0.522

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.927

Gnomad4 OTH AF: 0.745

Alfa AF: 0.884 Hom.: 56629

Bravo AF: 0.685

Asia WGS AF: 0.689 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.69
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1462795; hg19: chr3-110692754;