chr1-117024426-A-G

Variant names:

• chr1-117024426-A-G
• rs4659344
• NM_001256106.3:c.2429-1083A>G

Variant summary

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

The NM_001256106.3(CD101):​c.2429-1083A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 152,026 control chromosomes in the GnomAD database, including 11,479 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 0.38 (11479 hom., cov: 33)
• Consequence: CD101 NM_001256106.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.57
• Publications: 2 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD101	NM_001256106.3	c.2429-1083A>G		intron_variant	Intron 7 of 9	ENST00000682167.1	NP_001243035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD101	ENST00000682167.1	c.2429-1083A>G		intron_variant	Intron 7 of 9		NM_001256106.3	ENSP00000508039.1
CD101	ENST00000369470.1	c.2429-1083A>G		intron_variant	Intron 7 of 9	1		ENSP00000358482.1
CD101	ENST00000256652.8	c.2429-1083A>G		intron_variant	Intron 7 of 8	2		ENSP00000256652.4

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57684 AN: 151908 Hom.: 11445 Cov.: 33

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.357

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.380 AC: 57753 AN: 152026 Hom.: 11479 Cov.: 33 AF XY: 0.391 AC XY: 29058 AN XY: 74338

African (AFR) AF: 0.366 AC: 15188 AN: 41474

American (AMR) AF: 0.471 AC: 7197 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3470

East Asian (EAS) AF: 0.616 AC: 3181 AN: 5164

South Asian (SAS) AF: 0.435 AC: 2100 AN: 4824

European-Finnish (FIN) AF: 0.459 AC: 4844 AN: 10544

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.338 AC: 22989 AN: 67966

Other (OTH) AF: 0.365 AC: 770 AN: 2112

Alfa AF: 0.251 Hom.: 612

Bravo AF: 0.381

Asia WGS AF: 0.541 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.17
DANN	Benign	0.28
PhyloP100		-3.6
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: rs4659344; hg19: chr1-117567048;