ENST00000867051.1:c.*1507T>C

Variant names:

• chr11-22813523-T-C
• rs3763947
• ENST00000867051.1:c.*1507T>C

Variant summary

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

The ENST00000867051.1(GAS2):​c.*1507T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 151,772 control chromosomes in the GnomAD database, including 4,755 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 (4755 hom., cov: 31)
• Consequence: GAS2 ENST00000867051.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.289
• Publications: 5 publications found

Genes affected

GAS2 (HGNC:4167): (growth arrest specific 2) The protein encoded by this gene is a caspase-3 substrate that plays a role in regulating microfilament and cell shape changes during apoptosis. It can also modulate cell susceptibility to p53-dependent apoptosis by inhibiting calpain activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2017]

GAS2 Gene-Disease associations (from GenCC):

• hearing loss disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• hearing loss, autosomal recessive 125

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000867051.1. 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
	GAS2	ENST00000867051.1		c.*1507T>C		3_prime_UTR	Exon 8 of 8	ENSP00000537110.1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32941 AN: 151654 Hom.: 4746 Cov.: 31

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.0407

Gnomad SAS AF: 0.0569

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.217 AC: 32991 AN: 151772 Hom.: 4755 Cov.: 31 AF XY: 0.213 AC XY: 15763 AN XY: 74164

African (AFR) AF: 0.412 AC: 17048 AN: 41382

American (AMR) AF: 0.138 AC: 2106 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.263 AC: 910 AN: 3464

East Asian (EAS) AF: 0.0408 AC: 210 AN: 5144

South Asian (SAS) AF: 0.0561 AC: 270 AN: 4812

European-Finnish (FIN) AF: 0.155 AC: 1625 AN: 10494

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10219 AN: 67912

Other (OTH) AF: 0.211 AC: 446 AN: 2114

Alfa AF: 0.182 Hom.: 569

Bravo AF: 0.228

Asia WGS AF: 0.101 AC: 352 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.76
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs3763947; hg19: chr11-22835069;