rs1886695

Variant names:

• chr20-35592613-G-A
• rs1886695
• ENST00000430275.6:n.2640+2864C>T

Variant summary

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

The ENST00000430275.6(ENSG00000293413):​n.2640+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: ENSG00000293413 ENST00000430275.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• Publications: 16 publications found

Genes affected

ENSG00000293413 (HGNC:):

FER1L4 (HGNC:15801): (fer-1 like family member 4 (pseudogene)) Predicted to enable metal ion binding activity. Predicted to be involved in plasma membrane organization. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FER1L4	NR_119376.1	n.2640+2864C>T		intron_variant	Intron 21 of 42

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293413	ENST00000430275.6	n.2640+2864C>T		intron_variant	Intron 21 of 25	5
ENSG00000293413	ENST00000611673.4	n.413+2864C>T		intron_variant	Intron 4 of 14	2
FER1L4	ENST00000615531.4	n.2572+2864C>T		intron_variant	Intron 21 of 44	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

African (AFR) AF: 0.555 AC: 22945 AN: 41344

American (AMR) AF: 0.777 AC: 11829 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2481 AN: 3466

East Asian (EAS) AF: 0.855 AC: 4410 AN: 5160

South Asian (SAS) AF: 0.649 AC: 3120 AN: 4806

European-Finnish (FIN) AF: 0.822 AC: 8674 AN: 10554

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53517 AN: 67980

Other (OTH) AF: 0.718 AC: 1510 AN: 2104

Alfa AF: 0.767 Hom.: 198017

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
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs1886695; hg19: chr20-34180535;