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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000383686.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NECTIN3-AS1	ENST00000383686.4	TSL:2	n.743-79697C>T		intron	N/A
	NECTIN3-AS1	ENST00000474769.7	TSL:3	n.304-79697C>T		intron	N/A
	NECTIN3-AS1	ENST00000476301.6	TSL:4	n.526-79697C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7637068;

hg19: chr3-110692374;