rs17750520

Positions:

• chr3-183905156-A-G

Variant summary

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

The ENST00000454440.6(CYP2AB1P):​n.911+304T>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 0.0094 in 152,356 control chromosomes in the GnomAD database, including 57 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 0.0094 (57 hom., cov: 32)
• Consequence: CYP2AB1P ENST00000454440.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.574

Genes affected

CYP2AB1P (HGNC:39975): (cytochrome P450 family 2 subfamily AB member 1, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0832 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
CYP2AB1P	ENST00000454440.6	n.911+304T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00941 AC: 1433 AN: 152238 Hom.: 57 Cov.: 32

Gnomad AFR AF: 0.00162

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0510

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.0901

Gnomad SAS AF: 0.00289

Gnomad FIN AF: 0.00151

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000706

Gnomad OTH AF: 0.0163

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

GnomAD4 genome AF: 0.00940 AC: 1432 AN: 152356 Hom.: 57 Cov.: 32 AF XY: 0.0112 AC XY: 831 AN XY: 74520

Gnomad4 AFR AF: 0.00161

Gnomad4 AMR AF: 0.0510

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.0899

Gnomad4 SAS AF: 0.00290

Gnomad4 FIN AF: 0.00151

Gnomad4 NFE AF: 0.000706

Gnomad4 OTH AF: 0.0156

Alfa AF: 0.0136 Hom.: 7

Bravo AF: 0.0151

Asia WGS AF: 0.0360 AC: 126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17750520; hg19: chr3-183622944;