rs11664559

Variant names:

• chr18-14294025-G-A
• rs11664559
• ENST00000577614.2:n.1897+43618G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-14294025-G-A
• chr18-14294025-G-T

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000577614.2(CYP4F35P):​n.1897+43618G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 144,086 control chromosomes in the GnomAD database, including 54 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 0.0020 (54 hom., cov: 28)
• Consequence: CYP4F35P ENST00000577614.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.784
• Publications: 1 publications found

Genes affected

CYP4F35P (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BS2: High Homozygotes in GnomAd4 at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYP4F35P	ENST00000577614.2	n.1897+43618G>A		intron_variant	Intron 9 of 12	5
CYP4F35P	ENST00000716198.1	n.131+30965G>A		intron_variant	Intron 1 of 4
CYP4F35P	ENST00000716199.1	n.185+28357G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.00201 AC: 289 AN: 143968 Hom.: 54 Cov.: 28

Gnomad AFR AF: 0.000709

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000970

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000646

Gnomad FIN AF: 0.000522

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00374

Gnomad OTH AF: 0.00103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00201 AC: 290 AN: 144086 Hom.: 54 Cov.: 28 AF XY: 0.00175 AC XY: 123 AN XY: 70180

African (AFR) AF: 0.000707 AC: 29 AN: 41000

American (AMR) AF: 0.000969 AC: 14 AN: 14452

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3168

East Asian (EAS) AF: 0.00 AC: 0 AN: 4996

South Asian (SAS) AF: 0.000862 AC: 4 AN: 4642

European-Finnish (FIN) AF: 0.000522 AC: 5 AN: 9572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 268

European-Non Finnish (NFE) AF: 0.00374 AC: 236 AN: 63122

Other (OTH) AF: 0.00102 AC: 2 AN: 1968

Alfa AF: 0.000652 Hom.: 107

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.69
PhyloP100		-0.78

Splicing

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

Other links and lift over

dbSNP: rs11664559; hg19: chr18-14294024;