chr17-2743054-A-G

Variant names:

• chr17-2743054-A-G
• rs2317225
• NM_001355573.2:c.-24+6357T>C

Variant summary

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

The NM_001355573.2(CCDC92B):​c.-24+6357T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,116 control chromosomes in the GnomAD database, including 13,544 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 0.42 (13544 hom., cov: 33)
• Consequence: CCDC92B NM_001355573.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 6 publications found

Genes affected

CCDC92B (HGNC:52279): (coiled-coil domain containing 92B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC92B	NM_001355573.2	c.-24+6357T>C		intron_variant	Intron 1 of 3	ENST00000614400.2	NP_001342502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC92B	ENST00000614400.2	c.-24+6357T>C		intron_variant	Intron 1 of 3	6	NM_001355573.2	ENSP00000509343.1

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63764 AN: 151998 Hom.: 13533 Cov.: 33

Gnomad AFR AF: 0.424

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.329

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.420 AC: 63813 AN: 152116 Hom.: 13544 Cov.: 33 AF XY: 0.418 AC XY: 31089 AN XY: 74352

African (AFR) AF: 0.424 AC: 17586 AN: 41508

American (AMR) AF: 0.342 AC: 5232 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1364 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2605 AN: 5176

South Asian (SAS) AF: 0.329 AC: 1590 AN: 4826

European-Finnish (FIN) AF: 0.509 AC: 5377 AN: 10566

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28589 AN: 67980

Other (OTH) AF: 0.400 AC: 844 AN: 2108

Alfa AF: 0.413 Hom.: 57956

Bravo AF: 0.410

Asia WGS AF: 0.376 AC: 1309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.0
DANN	Benign	0.54
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs2317225; hg19: chr17-2646348;