chr1-162867060-A-C

Variant names:

• chr1-162867060-A-C
• rs2805050
• NM_178550.6:c.-13+1593T>G

Variant summary

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

The NM_178550.6(CCDC190):​c.-13+1593T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 151,786 control chromosomes in the GnomAD database, including 56,964 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 0.86 (56964 hom., cov: 31)
• Consequence: CCDC190 NM_178550.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_178550.6	c.-13+1593T>G		intron_variant	Intron 1 of 3		NP_848645.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC190	ENST00000367910.5	c.-13+1593T>G		intron_variant	Intron 1 of 3	2		ENSP00000356886.1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130046 AN: 151672 Hom.: 56961 Cov.: 31

Gnomad AFR AF: 0.741

Gnomad AMI AF: 0.942

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.864

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

GnomAD4 genome AF: 0.857 AC: 130102 AN: 151786 Hom.: 56964 Cov.: 31 AF XY: 0.853 AC XY: 63283 AN XY: 74186

Gnomad4 AFR AF: 0.741

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.431

Gnomad4 SAS AF: 0.801

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.956

Gnomad4 OTH AF: 0.861

Alfa AF: 0.884 Hom.: 9595

Bravo AF: 0.839

Asia WGS AF: 0.599 AC: 2051 AN: 3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2805050; hg19: chr1-162836850;