1-160858495-C-T

Position:

• chr1-160858495-C-T

Variant summary

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

The NM_016382.4(CD244):​c.61+4122G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,026 control chromosomes in the GnomAD database, including 14,033 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 0.36 (14033 hom., cov: 31)
• Consequence: CD244 NM_016382.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391

Genes affected

CD244 (HGNC:18171): (CD244 molecule) This gene encodes a cell surface receptor expressed on natural killer (NK) cells (and some T cells) that mediate non-major histocompatibility complex (MHC) restricted killing. The interaction between NK-cell and target cells via this receptor is thought to modulate NK-cell cytolytic activity. Alternatively spliced transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD244	NM_016382.4	c.61+4122G>A		intron_variant		ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.61+4122G>A		intron_variant		1	NM_016382.4	ENSP00000357013	P2
CD244	ENST00000322302.7	c.61+4122G>A		intron_variant		1		ENSP00000313619
CD244	ENST00000368033.7	c.61+4122G>A		intron_variant		1		ENSP00000357012	A2
CD244	ENST00000492063.5	c.61+4122G>A		intron_variant, NMD_transcript_variant		2		ENSP00000432636

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55287 AN: 151908 Hom.: 13999 Cov.: 31

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.364 AC: 55384 AN: 152026 Hom.: 14033 Cov.: 31 AF XY: 0.363 AC XY: 26976 AN XY: 74284

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.274

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.381

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.318

Alfa AF: 0.216 Hom.: 4129

Bravo AF: 0.380

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.72

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: rs11265498; hg19: chr1-160828285;