1-160830690-T-C

Variant names:

• chr1-160830690-T-C
• rs485618
• NM_016382.4:c.*657A>G

Variant summary

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

The NM_016382.4(CD244):​c.*657A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,214 control chromosomes in the GnomAD database, including 23,380 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 0.54 (23373 hom., cov: 33)
  • Exomes 𝑓: 0.40 (7 hom.)
• Consequence: CD244 NM_016382.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 18 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016382.4. 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
	CD244	NM_016382.4	MANE Select	c.*657A>G		3_prime_UTR	Exon 9 of 9	NP_057466.1
	CD244	NM_001166663.2		c.*657A>G		3_prime_UTR	Exon 9 of 9	NP_001160135.1
	CD244	NM_001166664.2		c.*657A>G		3_prime_UTR	Exon 8 of 8	NP_001160136.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD244	ENST00000368034.9	TSL:1 MANE Select	c.*657A>G		3_prime_UTR	Exon 9 of 9	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82760 AN: 151984 Hom.: 23326 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.563

GnomAD4 exome AF: 0.398 AC: 43 AN: 108 Hom.: 7 Cov.: 0 AF XY: 0.424 AC XY: 28 AN XY: 66

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.333 AC: 12 AN: 36

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.429 AC: 30 AN: 70

Other (OTH) AF: 0.500 AC: 1 AN: 2

GnomAD4 genome AF: 0.545 AC: 82868 AN: 152106 Hom.: 23373 Cov.: 33 AF XY: 0.548 AC XY: 40733 AN XY: 74334

African (AFR) AF: 0.665 AC: 27600 AN: 41494

American (AMR) AF: 0.612 AC: 9350 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1887 AN: 3466

East Asian (EAS) AF: 0.709 AC: 3658 AN: 5160

South Asian (SAS) AF: 0.626 AC: 3014 AN: 4818

European-Finnish (FIN) AF: 0.484 AC: 5116 AN: 10574

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30705 AN: 67988

Other (OTH) AF: 0.564 AC: 1192 AN: 2114

Alfa AF: 0.486 Hom.: 31202

Bravo AF: 0.559

Asia WGS AF: 0.702 AC: 2444 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.3
DANN	Benign	0.69
PhyloP100		0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs485618; hg19: chr1-160800480;