19-15992170-C-G

Variant names:

• chr19-15992170-C-G
• rs17756963
• ENST00000589847.3:n.646G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000589847.3(CYP4F9P):​n.646G>C 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 0.173 in 222,750 control chromosomes in the GnomAD database, including 4,904 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 0.19 (3868 hom., cov: 32)
  • Exomes 𝑓: 0.14 (1036 hom.)
• Consequence: CYP4F9P ENST00000589847.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 2 publications found

Genes affected

CYP4F9P (HGNC:39940): (cytochrome P450 family 4 subfamily F member 9, pseudogene)

LOC124900424 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124900424		n.15992170C>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F9P	ENST00000589847.3	n.646G>C		non_coding_transcript_exon_variant	Exon 6 of 12	6

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28348 AN: 152010 Hom.: 3856 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.0902

Gnomad OTH AF: 0.172

GnomAD4 exome AF: 0.144 AC: 10175 AN: 70620 Hom.: 1036 Cov.: 0 AF XY: 0.137 AC XY: 5533 AN XY: 40430

African (AFR) AF: 0.368 AC: 684 AN: 1860

American (AMR) AF: 0.141 AC: 1148 AN: 8120

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 88 AN: 852

East Asian (EAS) AF: 0.459 AC: 1712 AN: 3732

South Asian (SAS) AF: 0.173 AC: 1246 AN: 7218

European-Finnish (FIN) AF: 0.140 AC: 1860 AN: 13290

Middle Eastern (MID) AF: 0.105 AC: 178 AN: 1700

European-Non Finnish (NFE) AF: 0.0938 AC: 2943 AN: 31374

Other (OTH) AF: 0.128 AC: 316 AN: 2474

GnomAD4 genome AF: 0.187 AC: 28403 AN: 152130 Hom.: 3868 Cov.: 32 AF XY: 0.187 AC XY: 13882 AN XY: 74376

African (AFR) AF: 0.355 AC: 14735 AN: 41460

American (AMR) AF: 0.131 AC: 2005 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2323 AN: 5164

South Asian (SAS) AF: 0.176 AC: 850 AN: 4824

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10592

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0903 AC: 6138 AN: 68010

Other (OTH) AF: 0.174 AC: 367 AN: 2112

Alfa AF: 0.0329 Hom.: 27

Bravo AF: 0.195

Asia WGS AF: 0.350 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.43
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs17756963; hg19: chr19-16102980;