NM_001256106.3:c.2808C>A

Variant names:

• chr1-117025888-C-A
• rs138020050
• NM_001256106.3:c.2808C>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Moderate BP6_Moderate BP7 BS2

The NM_001256106.3(CD101):​c.2808C>A​(p.Leu936Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000811 in 1,609,742 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.00065 (1 hom., cov: 32)
  • Exomes 𝑓: 0.00083 (8 hom.)
• Consequence: CD101 NM_001256106.3 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.894
• Publications: 0 publications found

Genes affected

CD101 (HGNC:5949): (CD101 molecule) Predicted to enable hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides. Predicted to be involved in cell surface receptor signaling pathway. Predicted to act upstream of or within positive regulation of myeloid leukocyte differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

CD101-AS1 (HGNC:55665): (CD101 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP6: Variant 1-117025888-C-A is Benign according to our data. Variant chr1-117025888-C-A is described in ClinVar as Benign. ClinVar VariationId is 728720.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.894 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 8 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001256106.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD101	NM_001256106.3	MANE Select	c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 10	NP_001243035.1	Q93033
	CD101	NM_001256109.3		c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 10	NP_001243038.1	Q93033
	CD101	NM_004258.6		c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 10	NP_004249.2	Q93033

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD101	ENST00000682167.1	MANE Select	c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 10	ENSP00000508039.1	Q93033
	CD101	ENST00000369470.1	TSL:1	c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 10	ENSP00000358482.1	Q93033
	CD101	ENST00000256652.8	TSL:2	c.2808C>A	p.Leu936Leu	synonymous	Exon 8 of 9	ENSP00000256652.4	Q93033

Frequencies

GnomAD3 genomes AF: 0.000657 AC: 100 AN: 152154 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000145

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00747

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000632

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.00114 AC: 285 AN: 248950 AF XY: 0.00153

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000435

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000518

Gnomad OTH exome AF: 0.00115

GnomAD4 exome AF: 0.000827 AC: 1206 AN: 1457470 Hom.: 8 Cov.: 31 AF XY: 0.00101 AC XY: 735 AN XY: 724366

African (AFR) AF: 0.0000598 AC: 2 AN: 33424

American (AMR) AF: 0.000448 AC: 20 AN: 44642

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25918

East Asian (EAS) AF: 0.00 AC: 0 AN: 39608

South Asian (SAS) AF: 0.00644 AC: 554 AN: 85996

European-Finnish (FIN) AF: 0.0000187 AC: 1 AN: 53334

Middle Eastern (MID) AF: 0.00505 AC: 29 AN: 5746

European-Non Finnish (NFE) AF: 0.000484 AC: 537 AN: 1108626

Other (OTH) AF: 0.00105 AC: 63 AN: 60176

GnomAD4 genome AF: 0.000650 AC: 99 AN: 152272 Hom.: 1 Cov.: 32 AF XY: 0.000752 AC XY: 56 AN XY: 74456

African (AFR) AF: 0.000144 AC: 6 AN: 41552

American (AMR) AF: 0.000523 AC: 8 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5180

South Asian (SAS) AF: 0.00726 AC: 35 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10620

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000632 AC: 43 AN: 68016

Other (OTH) AF: 0.00284 AC: 6 AN: 2114

Alfa AF: 0.000508 Hom.: 0

Bravo AF: 0.000419

EpiCase AF: 0.000927

EpiControl AF: 0.00101

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	7.6
DANN	Benign	0.65
PhyloP100		0.89
Mutation Taster		=99/1	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs138020050; hg19: chr1-117568510;