rs646816

Variant names:

• chr19-15584290-T-G
• rs646816

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 0.0969 in 249,662 control chromosomes in the GnomAD database, including 1,358 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 0.096 (756 hom., cov: 32)
  • Exomes 𝑓: 0.098 (602 hom.)
• Consequence: CYP4F23P intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 5 publications found

Genes affected

CYP4F23P (HGNC:39944): (cytochrome P450 family 4 subfamily F member 23, pseudogene)

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 (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593402.6. 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
	CYP4F23P	ENST00000593402.6	TSL:6	n.1409+84T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0960 AC: 14596 AN: 152018 Hom.: 755 Cov.: 32

Gnomad AFR AF: 0.0828

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.0463

Gnomad ASJ AF: 0.102

Gnomad EAS AF: 0.0404

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0846

GnomAD4 exome AF: 0.0984 AC: 9596 AN: 97526 Hom.: 602 AF XY: 0.106 AC XY: 5851 AN XY: 55208

African (AFR) AF: 0.0708 AC: 143 AN: 2020

American (AMR) AF: 0.0292 AC: 169 AN: 5794

Ashkenazi Jewish (ASJ) AF: 0.0722 AC: 148 AN: 2050

East Asian (EAS) AF: 0.0310 AC: 173 AN: 5572

South Asian (SAS) AF: 0.178 AC: 2450 AN: 13784

European-Finnish (FIN) AF: 0.108 AC: 675 AN: 6232

Middle Eastern (MID) AF: 0.0969 AC: 37 AN: 382

European-Non Finnish (NFE) AF: 0.0944 AC: 5363 AN: 56806

Other (OTH) AF: 0.0896 AC: 438 AN: 4886

GnomAD4 genome AF: 0.0960 AC: 14606 AN: 152136 Hom.: 756 Cov.: 32 AF XY: 0.0965 AC XY: 7178 AN XY: 74366

African (AFR) AF: 0.0827 AC: 3430 AN: 41496

American (AMR) AF: 0.0462 AC: 706 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.102 AC: 354 AN: 3470

East Asian (EAS) AF: 0.0401 AC: 208 AN: 5184

South Asian (SAS) AF: 0.200 AC: 960 AN: 4806

European-Finnish (FIN) AF: 0.116 AC: 1231 AN: 10584

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7450 AN: 67990

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.113 Hom.: 542

Bravo AF: 0.0877

Asia WGS AF: 0.128 AC: 443 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	1.7
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs646816; hg19: chr19-15695101;