1-162852981-A-G

Variant names:

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

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394065.1(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_001394065.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_001394065.1	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000367912.7	NP_001380994.1
CCDC190	NM_178550.6	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4		NP_848645.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC190	ENST00000367912	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4	5	NM_001394065.1	ENSP00000356888.3
CCDC190	ENST00000524691.1	n.152+2651T>C		intron_variant	Intron 1 of 1	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

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000179

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.75

Splicing

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr1-162822771;