3-48445644-C-A

Position:

• chr3-48445644-C-A

Variant summary

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

The ENST00000438872.1(ENSG00000244380):​n.374+615G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 152,210 control chromosomes in the GnomAD database, including 5,696 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 0.25 (5696 hom., cov: 33)
• Consequence: ENST00000438872.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC51	XM_011534113.3	c.-14+615G>T		intron_variant			XP_011532415.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000438872.1	n.374+615G>T		intron_variant, non_coding_transcript_variant		3
	ENST00000435578.1	n.324-479G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.250 AC: 37982 AN: 152092 Hom.: 5686 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.382

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.634

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.250 AC: 38009 AN: 152210 Hom.: 5696 Cov.: 33 AF XY: 0.255 AC XY: 18986 AN XY: 74412

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.382

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.634

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.254

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.277

Alfa AF: 0.268 Hom.: 10307

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.9
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs730566; hg19: chr3-48487048;