3-149259527-A-G

Variant names:

• chr3-149259527-A-G
• rs7617219

Variant summary

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

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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000461341.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPHL1P	ENST00000461341.2	TSL:6	n.1210-1938T>C		intron	N/A

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

African (AFR) AF: 0.819 AC: 33959 AN: 41474

American (AMR) AF: 0.509 AC: 7779 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.485 AC: 1680 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2172 AN: 5152

South Asian (SAS) AF: 0.466 AC: 2236 AN: 4802

European-Finnish (FIN) AF: 0.386 AC: 4069 AN: 10552

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.390 AC: 26494 AN: 67918

Other (OTH) AF: 0.513 AC: 1083 AN: 2110

Alfa AF: 0.432 Hom.: 58334

Bravo AF: 0.549

Asia WGS AF: 0.476 AC: 1655 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.41
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7617219; hg19: chr3-148977314;