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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2A7P1		n.41026221C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2A7P1	ENST00000595391.1	n.339-66G>T		intron_variant	Intron 2 of 4	6
ENSG00000294932	ENST00000726877.1	n.231+80C>A		intron_variant	Intron 1 of 2
ENSG00000294932	ENST00000726878.1	n.222+80C>A		intron_variant	Intron 1 of 1
ENSG00000294953	ENST00000726968.1	n.*247G>T		downstream_gene_variant

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 v4.3

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;