rs3766377

Variant names:

• chr1-160830769-A-G
• rs3766377
• NM_016382.4:c.*578T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_016382.4(CD244):​c.*578T>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 0.333 in 153,088 control chromosomes in the GnomAD database, including 9,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.33 (9138 hom., cov: 33)
  • Exomes 𝑓: 0.26 (43 hom.)
• Consequence: CD244 NM_016382.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -1.15
• Publications: 17 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 -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 1-160830769-A-G is Benign according to our data. Variant chr1-160830769-A-G is described in ClinVar as Benign. ClinVar VariationId is 1232419.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD244	NM_016382.4	c.*578T>C		3_prime_UTR_variant	Exon 9 of 9	ENST00000368034.9	NP_057466.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD244	ENST00000368034.9	c.*578T>C		3_prime_UTR_variant	Exon 9 of 9	1	NM_016382.4	ENSP00000357013.4

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50682 AN: 151960 Hom.: 9116 Cov.: 33

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.348

GnomAD4 exome AF: 0.263 AC: 266 AN: 1010 Hom.: 43 Cov.: 0 AF XY: 0.294 AC XY: 149 AN XY: 506

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.432 AC: 63 AN: 146

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.280 AC: 14 AN: 50

South Asian (SAS) AF: 0.300 AC: 18 AN: 60

European-Finnish (FIN) AF: 1.00 AC: 2 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.222 AC: 160 AN: 720

Other (OTH) AF: 0.321 AC: 9 AN: 28

GnomAD4 genome AF: 0.334 AC: 50757 AN: 152078 Hom.: 9138 Cov.: 33 AF XY: 0.336 AC XY: 24977 AN XY: 74356

African (AFR) AF: 0.470 AC: 19493 AN: 41466

American (AMR) AF: 0.404 AC: 6175 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1221 AN: 3470

East Asian (EAS) AF: 0.328 AC: 1692 AN: 5166

South Asian (SAS) AF: 0.311 AC: 1501 AN: 4820

European-Finnish (FIN) AF: 0.304 AC: 3213 AN: 10586

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16523 AN: 67972

Other (OTH) AF: 0.345 AC: 729 AN: 2110

Alfa AF: 0.279 Hom.: 10985

Bravo AF: 0.351

Asia WGS AF: 0.349 AC: 1212 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Oct 28, 2020

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is associated with the following publications: (PMID: 26296604) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.56
PhyloP100		-1.1
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: rs3766377; hg19: chr1-160800559;