rs6511901

Positions:

• chr19-13916839-C-T

Variant summary

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

The NM_017721.5(CC2D1A):​c.749-1231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,964 control chromosomes in the GnomAD database, including 16,107 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 0.38 (16107 hom., cov: 32)
• Consequence: CC2D1A NM_017721.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430

Genes affected

CC2D1A (HGNC:30237): (coiled-coil and C2 domain containing 1A) This gene encodes a transcriptional repressor that binds to a conserved 14-bp 5'-repressor element and regulates expression of the 5-hydroxytryptamine (serotonin) receptor 1A gene in neuronal cells. The DNA binding and transcriptional repressor activities of the protein are inhibited by calcium. A mutation in this gene results in a nonsyndromic form of cognitive disability (MRT3). [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.778 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CC2D1A	NM_017721.5	c.749-1231C>T		intron_variant		ENST00000318003.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CC2D1A	ENST00000318003.11	c.749-1231C>T		intron_variant		1	NM_017721.5	P3
CC2D1A	ENST00000589606.5	c.749-1231C>T		intron_variant		1		A1
CC2D1A	ENST00000586955.5	c.286-1231C>T		intron_variant, NMD_transcript_variant		1
CC2D1A	ENST00000585896.5	n.806-1231C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.382 AC: 58031 AN: 151846 Hom.: 16048 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.0888

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.153

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.383 AC: 58155 AN: 151964 Hom.: 16107 Cov.: 32 AF XY: 0.378 AC XY: 28065 AN XY: 74290

Gnomad4 AFR AF: 0.785

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.171

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.153

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.337

Alfa AF: 0.262 Hom.: 3350

Bravo AF: 0.416

Asia WGS AF: 0.373 AC: 1293 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.87
DANN	Benign	0.41

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: rs6511901; hg19: chr19-14027652;