rs7944031

Positions:

• chr11-12907573-A-G

Variant summary

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

The NM_021961.6(TEAD1):​c.873+5460A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,098 control chromosomes in the GnomAD database, including 4,434 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 0.22 (4434 hom., cov: 32)
• Consequence: TEAD1 NM_021961.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

Genes affected

TEAD1 (HGNC:11714): (TEA domain transcription factor 1) This gene encodes a ubiquitous transcriptional enhancer factor that is a member of the TEA/ATTS domain family. This protein directs the transactivation of a wide variety of genes and, in placental cells, also acts as a transcriptional repressor. Mutations in this gene cause Sveinsson's chorioretinal atrophy. Additional transcript variants have been described but their full-length natures have not been experimentally verified. [provided by RefSeq, May 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TEAD1	NM_021961.6	c.873+5460A>G		intron_variant		ENST00000527636.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TEAD1	ENST00000527636.7	c.873+5460A>G		intron_variant		1	NM_021961.6
TEAD1	ENST00000334310.10	c.667-17339A>G		intron_variant		1		P1
TEAD1	ENST00000526600.1	c.585+5460A>G		intron_variant		1
TEAD1	ENST00000527575.6	c.700-17339A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.215 AC: 32704 AN: 151980 Hom.: 4437 Cov.: 32

Gnomad AFR AF: 0.306

Gnomad AMI AF: 0.0855

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.0992

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.192

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

GnomAD4 genome AF: 0.215 AC: 32732 AN: 152098 Hom.: 4434 Cov.: 32 AF XY: 0.221 AC XY: 16398 AN XY: 74326

Gnomad4 AFR AF: 0.306

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.0992

Gnomad4 EAS AF: 0.610

Gnomad4 SAS AF: 0.226

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.192

Alfa AF: 0.183 Hom.: 486

Bravo AF: 0.215

Asia WGS AF: 0.414 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.0
DANN	Benign	0.64

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: rs7944031; hg19: chr11-12929120;