chr4-182078968-G-T

Variant names:

• chr4-182078968-G-T
• rs10024819
• XM_017008385.2:c.-76+37225G>T

Variant summary

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

The ENST00000507869.7(TENM3-AS1):​n.521+2788C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,962 control chromosomes in the GnomAD database, including 6,962 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 0.30 (6962 hom., cov: 32)
• Consequence: TENM3-AS1 ENST00000507869.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.126
• Publications: 2 publications found

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]

TENM3-AS1 (HGNC:28076): (TENM3 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507869.7. 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
	TENM3-AS1	ENST00000507869.7	TSL:2	n.521+2788C>A		intron	N/A
	TENM3-AS1	ENST00000509012.5	TSL:4	n.220+2788C>A		intron	N/A
	TENM3-AS1	ENST00000669431.2		n.666+2788C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45506 AN: 151842 Hom.: 6956 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.297

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.300 AC: 45530 AN: 151962 Hom.: 6962 Cov.: 32 AF XY: 0.299 AC XY: 22174 AN XY: 74242

African (AFR) AF: 0.232 AC: 9613 AN: 41482

American (AMR) AF: 0.339 AC: 5177 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 947 AN: 3464

East Asian (EAS) AF: 0.322 AC: 1658 AN: 5148

South Asian (SAS) AF: 0.297 AC: 1425 AN: 4800

European-Finnish (FIN) AF: 0.330 AC: 3477 AN: 10550

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22198 AN: 67942

Other (OTH) AF: 0.295 AC: 621 AN: 2108

Alfa AF: 0.317 Hom.: 13081

Bravo AF: 0.301

Asia WGS AF: 0.270 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.6
DANN	Benign	0.66
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs10024819; hg19: chr4-183000121;