rs7637068

Variant names:

• chr3-110973527-G-A
• rs7637068
• ENST00000383686.4:n.743-79697C>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000383686.4(NECTIN3-AS1):​n.743-79697C>T variant causes a intron 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 ENST00000383686.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.192
• Publications: 2 publications found

Genes affected

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

LOC151760 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC151760	XR_007096272.1	n.484-79697C>T		intron_variant	Intron 2 of 3
LOC151760	XR_007096273.1	n.721-79697C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NECTIN3-AS1	ENST00000383686.4	n.743-79697C>T		intron_variant	Intron 2 of 3	2
NECTIN3-AS1	ENST00000474769.7	n.304-79697C>T		intron_variant	Intron 2 of 3	3
NECTIN3-AS1	ENST00000476301.6	n.526-79697C>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.438 AC: 18137 AN: 41440

American (AMR) AF: 0.222 AC: 3384 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 413 AN: 3468

East Asian (EAS) AF: 0.474 AC: 2440 AN: 5144

South Asian (SAS) AF: 0.126 AC: 606 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2079 AN: 10570

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4833 AN: 67974

Other (OTH) AF: 0.194 AC: 409 AN: 2108

Alfa AF: 0.114 Hom.: 7198

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7637068; hg19: chr3-110692374;