rs7313862

Positions:

• chr12-28458846-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018318.5(CCDC91):​c.1101+6192T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.337 in 151,946 control chromosomes in the GnomAD database, including 9,398 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 0.34 (9398 hom., cov: 31)
• Consequence: CCDC91 NM_018318.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

CCDC91 (HGNC:24855): (coiled-coil domain containing 91) Predicted to enable identical protein binding activity. Involved in Golgi to lysosome transport. Located in nucleoplasm and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC91	NM_018318.5	c.1101+6192T>C		intron_variant		ENST00000536442.6	NP_060788.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC91	ENST00000536442.6	c.1101+6192T>C		intron_variant		5	NM_018318.5	ENSP00000445660	P1

Frequencies

GnomAD3 genomes AF: 0.337 AC: 51127 AN: 151828 Hom.: 9386 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0468

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.337 AC: 51175 AN: 151946 Hom.: 9398 Cov.: 31 AF XY: 0.328 AC XY: 24347 AN XY: 74266

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.189

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.316

Alfa AF: 0.331 Hom.: 1363

Bravo AF: 0.339

Asia WGS AF: 0.135 AC: 474 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.1
DANN	Benign	0.61

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

Publications

LitVar

Other links and lift over

dbSNP: rs7313862; hg19: chr12-28611779;