rs1036429

Variant names:

• chr12-95877650-T-C
• rs1036429
• NM_182496.3:c.1278+561A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_182496.3(CCDC38):​c.1278+561A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.79 in 152,150 control chromosomes in the GnomAD database, including 47,946 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 0.79 (47946 hom., cov: 32)
• Consequence: CCDC38 NM_182496.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.931
• Publications: 32 publications found

Genes affected

CCDC38 (HGNC:26843): (coiled-coil domain containing 38) Located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

SNRPF (HGNC:11162): (small nuclear ribonucleoprotein polypeptide F) Enables RNA binding activity. Involved in spliceosomal snRNP assembly. Located in cytosol and nucleus. Part of several cellular components, including methylosome; nucleus; and pICln-Sm protein complex. Biomarker of nasopharynx carcinoma. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_182496.3. 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
	CCDC38	NM_182496.3	MANE Select	c.1278+561A>G		intron	N/A	NP_872302.2	Q502W7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC38	ENST00000344280.8	TSL:1 MANE Select	c.1278+561A>G		intron	N/A	ENSP00000345470.3	Q502W7
	SNRPF	ENST00000552085.1	TSL:3	c.130-2038T>C		intron	N/A	ENSP00000447127.1	F8W0W6
	SNRPF	ENST00000553192.5	TSL:4	c.130-2038T>C		intron	N/A	ENSP00000447751.1	A0A0B4J254

Frequencies

GnomAD3 genomes AF: 0.790 AC: 120105 AN: 152034 Hom.: 47909 Cov.: 32

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.755

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.790

Gnomad OTH AF: 0.776

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

GnomAD4 genome AF: 0.790 AC: 120192 AN: 152150 Hom.: 47946 Cov.: 32 AF XY: 0.793 AC XY: 58944 AN XY: 74376

African (AFR) AF: 0.839 AC: 34805 AN: 41500

American (AMR) AF: 0.632 AC: 9644 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2312 AN: 3470

East Asian (EAS) AF: 0.762 AC: 3937 AN: 5166

South Asian (SAS) AF: 0.798 AC: 3843 AN: 4816

European-Finnish (FIN) AF: 0.887 AC: 9410 AN: 10604

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.790 AC: 53706 AN: 68004

Other (OTH) AF: 0.776 AC: 1643 AN: 2116

Alfa AF: 0.782 Hom.: 72739

Bravo AF: 0.771

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.83
DANN	Benign	0.66
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1036429; hg19: chr12-96271428;