chr2-85693206-T-C

Variant names:

• chr2-85693206-T-C
• rs2886767
• ENST00000488945.5:n.48-2114T>C

Variant summary

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

The ENST00000488945.5(GNLY):​n.48-2114T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,530 control chromosomes in the GnomAD database, including 7,855 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 (7855 hom., cov: 31)
• Consequence: GNLY ENST00000488945.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 12 publications found

Genes affected

GNLY (HGNC:4414): (granulysin) The product of this gene is a member of the saposin-like protein (SAPLIP) family and is located in the cytotoxic granules of T cells, which are released upon antigen stimulation. This protein is present in cytotoxic granules of cytotoxic T lymphocytes and natural killer cells, and it has antimicrobial activity against M. tuberculosis and other organisms. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ENSG00000310473 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488945.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GNLY	ENST00000488945.5	TSL:1	n.48-2114T>C		intron	N/A
	ENSG00000310473	ENST00000850261.1		n.932+4264A>G		intron	N/A
	ENSG00000310473	ENST00000850262.1		n.567+4264A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44694 AN: 151452 Hom.: 7854 Cov.: 31

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.413

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.295 AC: 44685 AN: 151530 Hom.: 7855 Cov.: 31 AF XY: 0.295 AC XY: 21847 AN XY: 73960

African (AFR) AF: 0.0979 AC: 4044 AN: 41300

American (AMR) AF: 0.369 AC: 5601 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1538 AN: 3468

East Asian (EAS) AF: 0.581 AC: 2989 AN: 5142

South Asian (SAS) AF: 0.358 AC: 1717 AN: 4796

European-Finnish (FIN) AF: 0.308 AC: 3210 AN: 10432

Middle Eastern (MID) AF: 0.407 AC: 118 AN: 290

European-Non Finnish (NFE) AF: 0.358 AC: 24319 AN: 67888

Other (OTH) AF: 0.352 AC: 742 AN: 2106

Alfa AF: 0.323 Hom.: 1091

Bravo AF: 0.295

Asia WGS AF: 0.434 AC: 1506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.1
DANN	Benign	0.88
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2886767; hg19: chr2-85920329;