rs9394299

Variant names:

• chr6-35481549-C-G
• rs9394299
• NM_003214.4:c.268-1175G>C

Your query was ambiguous. Multiple possible variants found:

• chr6-35481549-C-G
• chr6-35481549-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_003214.4(TEAD3):​c.268-1175G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: TEAD3 NM_003214.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64

Genes affected

TEAD3 (HGNC:11716): (TEA domain transcription factor 3) This gene product is a member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain. It is predominantly expressed in the placenta and is involved in the transactivation of the chorionic somatomammotropin-B gene enhancer. Translation of this protein is initiated at a non-AUG (AUA) start codon. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TEAD3	NM_003214.4	c.268-1175G>C		intron_variant	Intron 3 of 12	ENST00000338863.13	NP_003205.2
TEAD3	NM_001395214.1	c.268-1427G>C		intron_variant	Intron 3 of 12		NP_001382143.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TEAD3	ENST00000338863.13	c.268-1175G>C		intron_variant	Intron 3 of 12	1	NM_003214.4	ENSP00000345772.8
TEAD3	ENST00000639578.3	c.268-1427G>C		intron_variant	Intron 3 of 12	1		ENSP00000492431.3
TEAD3	ENST00000402886.9	n.203-2233G>C		intron_variant	Intron 2 of 10	1		ENSP00000384577.5

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0040
DANN	Benign	0.46

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9394299; hg19: chr6-35449326;