rs7637068

Positions:

• chr3-110973527-G-A
• chr3-110973527-G-T

Variant summary

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

The ENST00000485473.2(NECTIN3-AS1):​n.242-79697C>T 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 0.214 in 151,982 control chromosomes in the GnomAD database, including 5,518 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 0.21 (5518 hom., cov: 32)
• Consequence: NECTIN3-AS1 ENST00000485473.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.459 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC151760	XR_007096272.1	n.484-79697C>T		intron_variant, non_coding_transcript_variant
LOC151760	XR_007096273.1	n.721-79697C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NECTIN3-AS1	ENST00000485473.2	n.242-79697C>T		intron_variant, non_coding_transcript_variant		3
NECTIN3-AS1	ENST00000474769.6	n.242-79697C>T		intron_variant, non_coding_transcript_variant		3
NECTIN3-AS1	ENST00000476301.5	n.503-79697C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32435 AN: 151864 Hom.: 5506 Cov.: 32

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.474

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0711

Gnomad OTH AF: 0.198

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

GnomAD4 genome AF: 0.214 AC: 32486 AN: 151982 Hom.: 5518 Cov.: 32 AF XY: 0.220 AC XY: 16319 AN XY: 74296

Gnomad4 AFR AF: 0.438

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.474

Gnomad4 SAS AF: 0.126

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.194

Alfa AF: 0.0876 Hom.: 1556

Bravo AF: 0.230

Asia WGS AF: 0.283 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7637068; hg19: chr3-110692374;