1-162852981-A-G

Variant names:

• chr1-162852981-A-G
• rs2684878
• NM_001394065.1:c.*1784T>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_178550.6(CCDC190):​c.*1784T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000163 in 614,660 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)
  • Exomes 𝑓: 0.0000016 (0 hom.)
• Consequence: CCDC190 NM_178550.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 0 publications found

Genes affected

CCDC190 (HGNC:28736): (coiled-coil domain containing 190)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178550.6. 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
	CCDC190	NM_001394065.1	MANE Select	c.*1784T>C		3_prime_UTR	Exon 4 of 4	NP_001380994.1
	CCDC190	NM_178550.6		c.*1784T>C		3_prime_UTR	Exon 4 of 4	NP_848645.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC190	ENST00000367912.7	TSL:5 MANE Select	c.*1784T>C		3_prime_UTR	Exon 4 of 4	ENSP00000356888.3
	CCDC190	ENST00000524691.1	TSL:1	n.152+2651T>C		intron	N/A
	CCDC190	ENST00000876170.1		c.*1784T>C		3_prime_UTR	Exon 4 of 4	ENSP00000546229.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.00000163 AC: 1 AN: 614660 Hom.: 0 Cov.: 8 AF XY: 0.00000308 AC XY: 1 AN XY: 324240

African (AFR) AF: 0.00 AC: 0 AN: 15948

American (AMR) AF: 0.00 AC: 0 AN: 29430

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 18102

East Asian (EAS) AF: 0.00 AC: 0 AN: 31686

South Asian (SAS) AF: 0.0000179 AC: 1 AN: 55792

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46110

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3662

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 382210

Other (OTH) AF: 0.00 AC: 0 AN: 31720

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.75
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2684878; hg19: chr1-162822771;