chr19-41025463-T-G

Variant names:

• chr19-41025463-T-G
• rs11666982

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 0.535 in 610,374 control chromosomes in the GnomAD database, including 93,093 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 0.58 (27899 hom., cov: 25)
  • Exomes 𝑓: 0.52 (65194 hom.)
• Consequence: CYP2A7P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0540
• Publications: 12 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.823 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CYP2A7P1		n.41025463T>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP2A7P1	ENST00000595391.1	n.646+137A>C		intron_variant	Intron 4 of 4	6

Frequencies

GnomAD3 genomes AF: 0.583 AC: 87576 AN: 150290 Hom.: 27867 Cov.: 25

Gnomad AFR AF: 0.831

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.689

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.689

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.595

GnomAD4 exome AF: 0.520 AC: 239055 AN: 459964 Hom.: 65194 AF XY: 0.523 AC XY: 129291 AN XY: 247162

African (AFR) AF: 0.836 AC: 11862 AN: 14188

American (AMR) AF: 0.741 AC: 23012 AN: 31070

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 9539 AN: 15598

East Asian (EAS) AF: 0.413 AC: 11057 AN: 26750

South Asian (SAS) AF: 0.617 AC: 33367 AN: 54072

European-Finnish (FIN) AF: 0.453 AC: 13103 AN: 28924

Middle Eastern (MID) AF: 0.651 AC: 1415 AN: 2172

European-Non Finnish (NFE) AF: 0.466 AC: 122047 AN: 261676

Other (OTH) AF: 0.535 AC: 13653 AN: 25514

GnomAD4 genome AF: 0.583 AC: 87660 AN: 150410 Hom.: 27899 Cov.: 25 AF XY: 0.585 AC XY: 42911 AN XY: 73342

African (AFR) AF: 0.831 AC: 33908 AN: 40810

American (AMR) AF: 0.689 AC: 10411 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 2101 AN: 3462

East Asian (EAS) AF: 0.386 AC: 1936 AN: 5014

South Asian (SAS) AF: 0.614 AC: 2900 AN: 4722

European-Finnish (FIN) AF: 0.427 AC: 4418 AN: 10350

Middle Eastern (MID) AF: 0.693 AC: 201 AN: 290

European-Non Finnish (NFE) AF: 0.446 AC: 30188 AN: 67666

Other (OTH) AF: 0.595 AC: 1236 AN: 2078

Alfa AF: 0.494 Hom.: 80408

Bravo AF: 0.611

Asia WGS AF: 0.529 AC: 1838 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.37
DANN	Benign	0.37
PhyloP100		-0.054

Splicing

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

Other links and lift over

dbSNP: rs11666982; hg19: chr19-41531368;