rs1886695

Positions:

• chr20-35592613-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000611673.4(FER1L4):​n.413+2864C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.72 in 151,848 control chromosomes in the GnomAD database, including 40,277 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 0.72 (40277 hom., cov: 29)
• Consequence: FER1L4 ENST00000611673.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692

Genes affected

FER1L4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FER1L4	NR_119376.1	n.2640+2864C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FER1L4	ENST00000430275.6	n.2640+2864C>T		intron_variant		5
FER1L4	ENST00000611673.4	n.413+2864C>T		intron_variant		2
FER1L4	ENST00000615531.4	n.2572+2864C>T		intron_variant		6

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109364 AN: 151730 Hom.: 40264 Cov.: 29

Gnomad AFR AF: 0.555

Gnomad AMI AF: 0.790

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.855

Gnomad SAS AF: 0.651

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.720 AC: 109400 AN: 151848 Hom.: 40277 Cov.: 29 AF XY: 0.722 AC XY: 53576 AN XY: 74172

Gnomad4 AFR AF: 0.555

Gnomad4 AMR AF: 0.777

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.855

Gnomad4 SAS AF: 0.649

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.787

Gnomad4 OTH AF: 0.718

Alfa AF: 0.771 Hom.: 91971

Bravo AF: 0.716

Asia WGS AF: 0.665 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1886695; hg19: chr20-34180535;