8-87040169-T-C

Variant names:

• chr8-87040169-T-C
• rs2943177
• NM_173538.3:c.431+100415T>C

Variant summary

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

The NM_173538.3(CNBD1):​c.431+100415T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.864 in 152,194 control chromosomes in the GnomAD database, including 57,269 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 0.86 (57269 hom., cov: 32)
• Consequence: CNBD1 NM_173538.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 4 publications found

Genes affected

CNBD1 (HGNC:26663): (cyclic nucleotide binding domain containing 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.96 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CNBD1	NM_173538.3	c.431+100415T>C		intron_variant	Intron 4 of 10	ENST00000518476.6	NP_775809.1
CNBD1	XM_017013149.2	c.431+100415T>C		intron_variant	Intron 4 of 10		XP_016868638.1
CNBD1	XM_024447082.2	c.431+100415T>C		intron_variant	Intron 4 of 6		XP_024302850.1
CNBD1	XM_047421411.1	c.266+100415T>C		intron_variant	Intron 3 of 6		XP_047277367.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CNBD1	ENST00000518476.6	c.431+100415T>C		intron_variant	Intron 4 of 10	1	NM_173538.3	ENSP00000430073.1
CNBD1	ENST00000523299.6	c.431+100415T>C		intron_variant	Intron 4 of 12	3		ENSP00000430986.2

Frequencies

GnomAD3 genomes AF: 0.864 AC: 131367 AN: 152076 Hom.: 57207 Cov.: 32

Gnomad AFR AF: 0.968

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.818

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.843

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.864 AC: 131490 AN: 152194 Hom.: 57269 Cov.: 32 AF XY: 0.858 AC XY: 63816 AN XY: 74400

African (AFR) AF: 0.968 AC: 40233 AN: 41574

American (AMR) AF: 0.851 AC: 13012 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.818 AC: 2841 AN: 3472

East Asian (EAS) AF: 0.637 AC: 3279 AN: 5148

South Asian (SAS) AF: 0.757 AC: 3639 AN: 4808

European-Finnish (FIN) AF: 0.790 AC: 8354 AN: 10572

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.842 AC: 57293 AN: 68006

Other (OTH) AF: 0.860 AC: 1817 AN: 2114

Alfa AF: 0.847 Hom.: 89462

Bravo AF: 0.870

Asia WGS AF: 0.717 AC: 2496 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	0.90
DANN	Benign	0.53
PhyloP100		-1.9
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: rs2943177; hg19: chr8-88052397;