19-50725314-C-CGCCCA

Position:

• chr19-50725314-C-CGCCCA

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_002975.3(CLEC11A):​c.827_831dup​(p.Ala278ProfsTer129) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,611,922 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0015 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0020 (12 hom.)
• Consequence: CLEC11A NM_002975.3 frameshift
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0370

Genes affected

CLEC11A (HGNC:10576): (C-type lectin domain containing 11A) This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• BP6: Variant 19-50725314-C-CGCCCA is Benign according to our data. Variant chr19-50725314-C-CGCCCA is described in ClinVar as [Likely_benign]. Clinvar id is 785833.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLEC11A	NM_002975.3	c.827_831dup	p.Ala278ProfsTer129	frameshift_variant	4/4	ENST00000250340.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CLEC11A	ENST00000250340.9	c.827_831dup	p.Ala278ProfsTer129	frameshift_variant	4/4	1	NM_002975.3	P1
CLEC11A	ENST00000599973.1	c.876_880dup	p.Arg294ProfsTer49	frameshift_variant	4/4	1

Frequencies

GnomAD3 genomes AF: 0.00156 AC: 237 AN: 152202 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00124

Gnomad ASJ AF: 0.00778

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00257

Gnomad OTH AF: 0.00192

GnomAD3 exomes AF: 0.00166 AC: 391 AN: 236204 Hom.: 4 AF XY: 0.00174 AC XY: 227 AN XY: 130194

Gnomad AFR exome AF: 0.000144

Gnomad AMR exome AF: 0.00158

Gnomad ASJ exome AF: 0.00723

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000990

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00234

Gnomad OTH exome AF: 0.00328

GnomAD4 exome AF: 0.00203 AC: 2956 AN: 1459606 Hom.: 12 Cov.: 48 AF XY: 0.00201 AC XY: 1461 AN XY: 726132

Gnomad4 AFR exome AF: 0.000269

Gnomad4 AMR exome AF: 0.00166

Gnomad4 ASJ exome AF: 0.00794

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000128

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00224

Gnomad4 OTH exome AF: 0.00224

GnomAD4 genome AF: 0.00155 AC: 236 AN: 152316 Hom.: 2 Cov.: 33 AF XY: 0.00144 AC XY: 107 AN XY: 74484

Gnomad4 AFR AF: 0.000192

Gnomad4 AMR AF: 0.00124

Gnomad4 ASJ AF: 0.00778

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00257

Gnomad4 OTH AF: 0.00190

EpiCase AF: 0.00360

EpiControl AF: 0.00380

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Mar 29, 2018

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-51228571;