rs7753655

Variant names:

• chr6-49568851-A-G
• rs7753655

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 0.24 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 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662
• Publications: 2 publications found

Genes affected

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

ENSG00000301537 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000407830.1. 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
	CYP2AC1P	ENST00000407830.1	TSL:6	n.958+1690T>C		intron	N/A
	ENSG00000301537	ENST00000779575.1		n.357+2029A>G		intron	N/A
	ENSG00000301537	ENST00000779576.1		n.334-927A>G		intron	N/A

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

African (AFR) AF: 0.121 AC: 5014 AN: 41480

American (AMR) AF: 0.167 AC: 2547 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3472

East Asian (EAS) AF: 0.278 AC: 1435 AN: 5158

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4820

European-Finnish (FIN) AF: 0.281 AC: 2972 AN: 10572

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.319 AC: 21699 AN: 67962

Other (OTH) AF: 0.203 AC: 428 AN: 2108

Alfa AF: 0.289 Hom.: 2992

Bravo AF: 0.224

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.48
DANN	Benign	0.62
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs7753655; hg19: chr6-49536564;