rs1912453

chr1-162851501-A-G

Variant summary

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

The NM_001394065.1(CCDC190):c.*3264T>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 0.573 in 151,392 control chromosomes in the GnomAD database, including 24,977 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 0.57 (24967 hom., cov: 28)
  • Exomes 𝑓: 0.68 (10 hom.)
• Consequence: CCDC190 NM_001394065.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.362

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC190	NM_001394065.1	c.*3264T>C		3_prime_UTR_variant	4/4	ENST00000367912.7
CCDC190	NM_178550.6	c.*3264T>C		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC190	ENST00000367912.7	c.*3264T>C		3_prime_UTR_variant	4/4	5	NM_001394065.1	A2
CCDC190	ENST00000524691.1	n.152+4131T>C		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.573 AC: 86653 AN: 151230 Hom.: 24957 Cov.: 28

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.571

GnomAD4 exome AF: 0.682 AC: 30 AN: 44 Hom.: 10 Cov.: 0 AF XY: 0.706 AC XY: 24 AN XY: 34

Gnomad4 AMR exome AF: 0.500

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.667

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.573 AC: 86702 AN: 151348 Hom.: 24967 Cov.: 28 AF XY: 0.573 AC XY: 42354 AN XY: 73914

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.425

Gnomad4 SAS AF: 0.631

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.573

Alfa AF: 0.597 Hom.: 54868

Bravo AF: 0.567

Asia WGS AF: 0.520 AC: 1807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.4
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1912453; hg19: chr1-162821291;