chr6-49568851-A-G

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2AC1P		n.49568851A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2AC1P	ENST00000407830.1	n.958+1690T>C		intron_variant	Intron 6 of 6	6
ENSG00000301537	ENST00000779575.1	n.357+2029A>G		intron_variant	Intron 1 of 1
ENSG00000301537	ENST00000779576.1	n.334-927A>G		intron_variant	Intron 1 of 2
ENSG00000301553	ENST00000779679.1	n.128+1686T>C		intron_variant	Intron 1 of 1

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 v4.3

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;