rs7249735

Variant names:

• chr19-41025751-A-C
• rs7249735
• ENST00000595391.1:n.495T>G

Your query was ambiguous. Multiple possible variants found:

• chr19-41025751-A-C
• chr19-41025751-A-G
• chr19-41025751-A-T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000595391.1(CYP2A7P1):​n.495T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 773,298 control chromosomes in the GnomAD database, including 40,571 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 0.33 (8582 hom., cov: 31)
  • Exomes 𝑓: 0.31 (31989 hom.)
• Consequence: CYP2A7P1 ENST00000595391.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.97
• Publications: 11 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (REVEL=0.033).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.416 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2A7P1		n.41025751A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2A7P1	ENST00000595391.1	n.495T>G		non_coding_transcript_exon_variant	Exon 4 of 5	6
ENSG00000294932	ENST00000726877.1	n.-160A>C		upstream_gene_variant
ENSG00000294932	ENST00000726878.1	n.-169A>C		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49587 AN: 151610 Hom.: 8580 Cov.: 31

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.425

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.349

GnomAD2 exomes AF: 0.323 AC: 80751 AN: 250132 AF XY: 0.322

Gnomad AFR exome AF: 0.417

Gnomad AMR exome AF: 0.449

Gnomad ASJ exome AF: 0.397

Gnomad EAS exome AF: 0.157

Gnomad FIN exome AF: 0.226

Gnomad NFE exome AF: 0.289

Gnomad OTH exome AF: 0.320

GnomAD4 exome AF: 0.309 AC: 191968 AN: 621570 Hom.: 31989 Cov.: 3 AF XY: 0.312 AC XY: 105748 AN XY: 338428

African (AFR) AF: 0.421 AC: 7421 AN: 17646

American (AMR) AF: 0.448 AC: 19359 AN: 43242

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 8243 AN: 20758

East Asian (EAS) AF: 0.150 AC: 5323 AN: 35592

South Asian (SAS) AF: 0.401 AC: 27936 AN: 69750

European-Finnish (FIN) AF: 0.226 AC: 11747 AN: 51886

Middle Eastern (MID) AF: 0.382 AC: 1561 AN: 4088

European-Non Finnish (NFE) AF: 0.290 AC: 100255 AN: 346162

Other (OTH) AF: 0.312 AC: 10123 AN: 32446

GnomAD4 genome AF: 0.327 AC: 49614 AN: 151728 Hom.: 8582 Cov.: 31 AF XY: 0.326 AC XY: 24130 AN XY: 74102

African (AFR) AF: 0.404 AC: 16717 AN: 41330

American (AMR) AF: 0.425 AC: 6492 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3468

East Asian (EAS) AF: 0.163 AC: 840 AN: 5146

South Asian (SAS) AF: 0.382 AC: 1833 AN: 4800

European-Finnish (FIN) AF: 0.221 AC: 2323 AN: 10510

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 18998 AN: 67878

Other (OTH) AF: 0.352 AC: 743 AN: 2110

Alfa AF: 0.302 Hom.: 3672

Bravo AF: 0.344

Asia WGS AF: 0.306 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.7
DANN	Benign	0.24
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs7249735; hg19: chr19-41531656;