chr4-181947687-G-A

Position:

• chr4-181947687-G-A

Variant summary

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

The ENST00000509012.5(TENM3-AS1):​n.378+64975C>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 0.295 in 151,874 control chromosomes in the GnomAD database, including 7,278 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 0.29 (7278 hom., cov: 32)
• Consequence: TENM3-AS1 ENST00000509012.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.56

Genes affected

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

TENM3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TENM3	XM_017008385.2	c.-156+79855G>A		intron_variant
TENM3	XM_017008389.2	c.-156+79855G>A		intron_variant
TENM3	XM_017008390.2	c.-156+79855G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TENM3-AS1	ENST00000509012.5	n.378+64975C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44704 AN: 151756 Hom.: 7255 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.177

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.295 AC: 44768 AN: 151874 Hom.: 7278 Cov.: 32 AF XY: 0.289 AC XY: 21463 AN XY: 74230

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.202

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.254

Gnomad4 OTH AF: 0.283

Alfa AF: 0.260 Hom.: 10826

Bravo AF: 0.297

Asia WGS AF: 0.267 AC: 929 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9993255; hg19: chr4-182868840;