rs7255146

Variant names:

• chr19-41026221-C-A
• rs7255146

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 0.177 in 489,930 control chromosomes in the GnomAD database, including 8,932 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 0.20 (3603 hom., cov: 32)
  • Exomes 𝑓: 0.17 (5329 hom.)
• Consequence: CYP2A7P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0130
• Publications: 6 publications found

Genes affected

CYP2A7P1 (HGNC:2612): (cytochrome P450 family 2 subfamily A member 7 pseudogene 1)

ENSG00000294932 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000595391.1. 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
	CYP2A7P1	ENST00000595391.1	TSL:6	n.339-66G>T		intron	N/A
	ENSG00000294932	ENST00000726877.1		n.231+80C>A		intron	N/A
	ENSG00000294932	ENST00000726878.1		n.222+80C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30715 AN: 151876 Hom.: 3609 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.211

GnomAD4 exome AF: 0.166 AC: 55968 AN: 337936 Hom.: 5329 AF XY: 0.165 AC XY: 31306 AN XY: 189792

African (AFR) AF: 0.347 AC: 3395 AN: 9790

American (AMR) AF: 0.111 AC: 3105 AN: 27894

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 3242 AN: 12070

East Asian (EAS) AF: 0.0292 AC: 329 AN: 11256

South Asian (SAS) AF: 0.151 AC: 9147 AN: 60718

European-Finnish (FIN) AF: 0.138 AC: 2358 AN: 17028

Middle Eastern (MID) AF: 0.269 AC: 643 AN: 2390

European-Non Finnish (NFE) AF: 0.170 AC: 30696 AN: 180266

Other (OTH) AF: 0.185 AC: 3053 AN: 16524

GnomAD4 genome AF: 0.202 AC: 30724 AN: 151994 Hom.: 3603 Cov.: 32 AF XY: 0.197 AC XY: 14608 AN XY: 74318

African (AFR) AF: 0.320 AC: 13240 AN: 41376

American (AMR) AF: 0.161 AC: 2463 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 934 AN: 3470

East Asian (EAS) AF: 0.0386 AC: 199 AN: 5152

South Asian (SAS) AF: 0.141 AC: 680 AN: 4818

European-Finnish (FIN) AF: 0.130 AC: 1378 AN: 10586

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.164 AC: 11157 AN: 67990

Other (OTH) AF: 0.209 AC: 441 AN: 2110

Alfa AF: 0.184 Hom.: 3580

Bravo AF: 0.212

Asia WGS AF: 0.0880 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.4
DANN	Benign	0.81
PhyloP100		0.013

Splicing

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

Other links and lift over

dbSNP: rs7255146; hg19: chr19-41532126;