rs7753655

Positions:

• chr6-49568851-A-G

Variant summary

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

The ENST00000407830.1(CYP2AC1P):​n.958+1690T>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 0.24 in 152,044 control chromosomes in the GnomAD database, including 5,025 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 0.24 (5025 hom., cov: 31)
• Consequence: CYP2AC1P ENST00000407830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

Genes affected

CYP2AC1P (HGNC:39976): (cytochrome P450 family 2 subfamily AC member 1, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CYP2AC1P	ENST00000407830.1	n.958+1690T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36514 AN: 151924 Hom.: 5026 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.240 AC: 36534 AN: 152044 Hom.: 5025 Cov.: 31 AF XY: 0.239 AC XY: 17732 AN XY: 74330

Gnomad4 AFR AF: 0.121

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.278

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.203

Alfa AF: 0.290 Hom.: 2626

Bravo AF: 0.224

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7753655; hg19: chr6-49536564;