3-149259527-A-G

Position:

• chr3-149259527-A-G

Variant summary

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

The ENST00000461341.2(CPHL1P):​n.1210-1938T>C 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 0.527 in 151,944 control chromosomes in the GnomAD database, including 23,793 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 0.53 (23793 hom., cov: 32)
• Consequence: CPHL1P ENST00000461341.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792

Genes affected

CPHL1P (HGNC:31714): (ceruloplasmin and hephaestin like 1, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CPHL1P	ENST00000461341.2	n.1210-1938T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79964 AN: 151826 Hom.: 23741 Cov.: 32

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.527 AC: 80076 AN: 151944 Hom.: 23793 Cov.: 32 AF XY: 0.525 AC XY: 38988 AN XY: 74256

Gnomad4 AFR AF: 0.819

Gnomad4 AMR AF: 0.509

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.422

Gnomad4 SAS AF: 0.466

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.513

Alfa AF: 0.415 Hom.: 22073

Bravo AF: 0.549

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7617219; hg19: chr3-148977314;