11-22680004-T-C

Position:

• chr11-22680004-T-C

Variant summary

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

The NM_001143830.3(GAS2):​c.145+4990T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.925 in 152,088 control chromosomes in the GnomAD database, including 65,377 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 0.92 (65377 hom., cov: 32)
• Consequence: GAS2 NM_001143830.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GAS2	NM_001143830.3	c.145+4990T>C		intron_variant		ENST00000454584.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GAS2	ENST00000454584.7	c.145+4990T>C		intron_variant		1	NM_001143830.3	P1

Frequencies

GnomAD3 genomes AF: 0.925 AC: 140552 AN: 151970 Hom.: 65347 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.928

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 0.933

Gnomad SAS AF: 0.988

Gnomad FIN AF: 0.976

Gnomad MID AF: 0.987

Gnomad NFE AF: 0.971

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.925 AC: 140641 AN: 152088 Hom.: 65377 Cov.: 32 AF XY: 0.926 AC XY: 68829 AN XY: 74342

Gnomad4 AFR AF: 0.818

Gnomad4 AMR AF: 0.928

Gnomad4 ASJ AF: 0.988

Gnomad4 EAS AF: 0.933

Gnomad4 SAS AF: 0.988

Gnomad4 FIN AF: 0.976

Gnomad4 NFE AF: 0.971

Gnomad4 OTH AF: 0.942

Alfa AF: 0.945 Hom.: 8458

Bravo AF: 0.914

Asia WGS AF: 0.936 AC: 3250 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.4
DANN	Benign	0.69

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: rs426344; hg19: chr11-22701550;