NM_013269.6:c.357+91T>A

Variant names:

• chr12-9688177-T-A
• rs7310460
• NM_013269.6:c.357+91T>A

Variant summary

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

The NM_013269.6(CLEC2D):​c.357+91T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 1,277,960 control chromosomes in the GnomAD database, including 116,230 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 0.35 (10815 hom., cov: 29)
  • Exomes 𝑓: 0.43 (105415 hom.)
• Consequence: CLEC2D NM_013269.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 6 publications found

Genes affected

CLEC2D (HGNC:14351): (C-type lectin domain family 2 member D) This gene encodes a member of the natural killer cell receptor C-type lectin family. The encoded protein inhibits osteoclast formation and contains a transmembrane domain near the N-terminus as well as the C-type lectin-like extracellular domain. Several alternatively spliced transcript variants have been identified for this gene. [provided by RefSeq, Oct 2010]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.566 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLEC2D	NM_013269.6	c.357+91T>A		intron_variant	Intron 3 of 4	ENST00000290855.11	NP_037401.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLEC2D	ENST00000290855.11	c.357+91T>A		intron_variant	Intron 3 of 4	1	NM_013269.6	ENSP00000290855.6

Frequencies

GnomAD3 genomes AF: 0.354 AC: 52793 AN: 149010 Hom.: 10815 Cov.: 29

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.384

Gnomad EAS AF: 0.584

Gnomad SAS AF: 0.409

Gnomad FIN AF: 0.374

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.385

GnomAD4 exome AF: 0.427 AC: 482043 AN: 1128840 Hom.: 105415 Cov.: 22 AF XY: 0.427 AC XY: 232708 AN XY: 544726

African (AFR) AF: 0.129 AC: 2894 AN: 22446

American (AMR) AF: 0.519 AC: 6828 AN: 13164

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 6276 AN: 15706

East Asian (EAS) AF: 0.615 AC: 16287 AN: 26464

South Asian (SAS) AF: 0.395 AC: 13663 AN: 34584

European-Finnish (FIN) AF: 0.420 AC: 11665 AN: 27790

Middle Eastern (MID) AF: 0.362 AC: 1491 AN: 4124

European-Non Finnish (NFE) AF: 0.430 AC: 404229 AN: 939476

Other (OTH) AF: 0.415 AC: 18710 AN: 45086

GnomAD4 genome AF: 0.354 AC: 52809 AN: 149120 Hom.: 10815 Cov.: 29 AF XY: 0.355 AC XY: 25721 AN XY: 72524

African (AFR) AF: 0.147 AC: 6000 AN: 40678

American (AMR) AF: 0.432 AC: 6423 AN: 14880

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1323 AN: 3444

East Asian (EAS) AF: 0.584 AC: 2979 AN: 5102

South Asian (SAS) AF: 0.409 AC: 1953 AN: 4772

European-Finnish (FIN) AF: 0.374 AC: 3507 AN: 9380

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.433 AC: 29289 AN: 67602

Other (OTH) AF: 0.391 AC: 810 AN: 2070

Alfa AF: 0.396 Hom.: 1622

Bravo AF: 0.356

Asia WGS AF: 0.490 AC: 1701 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		-0.071
PromoterAI		-0.017	Neutral
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: rs7310460; hg19: chr12-9840773;