NM_001321759.2:c.101+207T>C

Variant names:

• chr15-36580168-T-C
• rs6495842
• NM_001321759.2:c.101+207T>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001321759.2(CDIN1):​c.101+207T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,252 control chromosomes in the GnomAD database, including 54,789 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.85 (54789 hom., cov: 33)
• Consequence: CDIN1 NM_001321759.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.154
• Publications: 4 publications found

Genes affected

CDIN1 (HGNC:26929): (CDAN1 interacting nuclease 1) This gene encodes a protein with two predicted helix-turn-helix domains. Mutations in this gene were found in families with congenital dyserythropoietic anemia type Ib. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]

CDIN1 Gene-Disease associations (from GenCC):

• congenital dyserythropoietic anemia type type 1B

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• congenital dyserythropoietic anemia type 1

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BP6: Variant 15-36580168-T-C is Benign according to our data. Variant chr15-36580168-T-C is described in ClinVar as Benign. ClinVar VariationId is 1244450.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001321759.2. 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
	CDIN1	NM_001321759.2	MANE Select	c.101+207T>C		intron	N/A	NP_001308688.1	Q9Y2V0-1
	CDIN1	NM_001321761.2		c.101+207T>C		intron	N/A	NP_001308690.1	H3BS01
	CDIN1	NM_001290233.2		c.101+207T>C		intron	N/A	NP_001277162.1	A0A2R8YD89

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDIN1	ENST00000566621.6	TSL:5 MANE Select	c.101+207T>C		intron	N/A	ENSP00000455397.1	Q9Y2V0-1
	CDIN1	ENST00000437989.6	TSL:1	c.101+207T>C		intron	N/A	ENSP00000401362.2	Q9Y2V0-1
	CDIN1	ENST00000569302.6	TSL:5	c.101+207T>C		intron	N/A	ENSP00000456477.1	H3BS01

Frequencies

GnomAD3 genomes AF: 0.847 AC: 128836 AN: 152134 Hom.: 54742 Cov.: 33

Gnomad AFR AF: 0.795

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.905

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.883

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.859

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

GnomAD4 genome AF: 0.847 AC: 128940 AN: 152252 Hom.: 54789 Cov.: 33 AF XY: 0.847 AC XY: 63047 AN XY: 74438

African (AFR) AF: 0.795 AC: 33040 AN: 41536

American (AMR) AF: 0.887 AC: 13568 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.905 AC: 3140 AN: 3470

East Asian (EAS) AF: 0.879 AC: 4545 AN: 5172

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4824

European-Finnish (FIN) AF: 0.883 AC: 9371 AN: 10608

Middle Eastern (MID) AF: 0.959 AC: 282 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58540 AN: 68018

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.847 Hom.: 7081

Bravo AF: 0.846

Asia WGS AF: 0.842 AC: 2928 AN: 3478

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	-0.98
CADD	Benign	14
DANN	Benign	0.72
PhyloP100		-0.15
PromoterAI		-0.032	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: rs6495842; hg19: chr15-36872369;