rs1979679

Positions:

• chr12-28253582-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.-14-3620T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,152 control chromosomes in the GnomAD database, including 5,265 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 0.25 (5265 hom., cov: 32)
• Consequence: CCDC91 NM_018318.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC91	NM_018318.5	c.-14-3620T>C		intron_variant		ENST00000536442.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC91	ENST00000536442.6	c.-14-3620T>C		intron_variant		5	NM_018318.5	P1

Frequencies

GnomAD3 genomes AF: 0.249 AC: 37902 AN: 152034 Hom.: 5258 Cov.: 32

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.334

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.567

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.261

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

GnomAD4 genome AF: 0.249 AC: 37929 AN: 152152 Hom.: 5265 Cov.: 32 AF XY: 0.254 AC XY: 18890 AN XY: 74374

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.287

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.359

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.240

Gnomad4 OTH AF: 0.261

Alfa AF: 0.247 Hom.: 8212

Bravo AF: 0.250

Asia WGS AF: 0.400 AC: 1386 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.52

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: rs1979679; hg19: chr12-28406515;