rs1036429

chr12-95877650-T-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC38	NM_182496.3	c.1278+561A>G		intron_variant		ENST00000344280.8
CCDC38	XM_011537883.3	c.1278+561A>G		intron_variant
CCDC38	XM_011537888.4	c.627+561A>G		intron_variant
CCDC38	XM_047428281.1	c.786+561A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC38	ENST00000344280.8	c.1278+561A>G		intron_variant		1	NM_182496.3	P1
SNRPF	ENST00000552085.1	c.130-2038T>C		intron_variant		3
SNRPF	ENST00000553192.5	c.130-2038T>C		intron_variant		4
CCDC38	ENST00000549876.5	c.164+561A>G		intron_variant, NMD_transcript_variant		5

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

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.887

Gnomad4 NFE AF: 0.790

Gnomad4 OTH AF: 0.776

Alfa AF: 0.779 Hom.: 44995

Bravo AF: 0.771

Asia WGS AF: 0.794 AC: 2761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.83
Dann	Benign	0.66

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: rs1036429; hg19: chr12-96271428;