rs7697691

Variant names:

• chr4-181695804-G-A
• rs7697691
• XM_017008385.2:c.-399-43683G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-181695804-G-A
• chr4-181695804-G-C

Variant summary

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

The XM_017008385.2(TENM3):​c.-399-43683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.797 in 152,144 control chromosomes in the GnomAD database, including 48,582 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 0.80 (48582 hom., cov: 33)
• Consequence: TENM3 XM_017008385.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.796

Genes affected

TENM3 (HGNC:29944): (teneurin transmembrane protein 3) This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]

ENSG00000287948 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TENM3	XM_017008385.2	c.-399-43683G>A		intron_variant	Intron 1 of 32		XP_016863874.1
TENM3	XM_047415933.1	c.-399-43683G>A		intron_variant	Intron 1 of 32		XP_047271889.1
TENM3	XM_017008389.2	c.-399-43683G>A		intron_variant	Intron 1 of 32		XP_016863878.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287948	ENST00000670601.1	n.124+4215C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.797 AC: 121221 AN: 152026 Hom.: 48533 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.797 AC: 121324 AN: 152144 Hom.: 48582 Cov.: 33 AF XY: 0.794 AC XY: 59075 AN XY: 74374

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.881

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.810

Alfa AF: 0.814 Hom.: 7962

Bravo AF: 0.804

Asia WGS AF: 0.744 AC: 2589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.083
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7697691; hg19: chr4-182616957;