20-35564866-C-T

Variant names:

• chr20-35564866-C-T
• rs2277862
• ENST00000611673.4:n.1047G>A

Variant summary

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

The ENST00000611673.4(ENSG00000293413):​n.1047G>A 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 0.175 in 455,700 control chromosomes in the GnomAD database, including 7,891 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 0.17 (2350 hom., cov: 32)
  • Exomes 𝑓: 0.18 (5541 hom.)
• Consequence: ENSG00000293413 ENST00000611673.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 100 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=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000611673.4. 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
	FER1L4	NR_119376.1		n.4574G>A		non_coding_transcript_exon	Exon 37 of 43

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293413	ENST00000611673.4	TSL:2	n.1047G>A		non_coding_transcript_exon	Exon 11 of 15
	ENSG00000293413	ENST00000613061.4	TSL:5	n.1397G>A		non_coding_transcript_exon	Exon 11 of 16
	FER1L4	ENST00000615531.4	TSL:6	n.4562G>A		non_coding_transcript_exon	Exon 37 of 45

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25435 AN: 152060 Hom.: 2350 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.142

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.187

GnomAD2 exomes AF: 0.184 AC: 25685 AN: 139410 AF XY: 0.190

Gnomad AFR exome AF: 0.197

Gnomad AMR exome AF: 0.182

Gnomad ASJ exome AF: 0.260

Gnomad EAS exome AF: 0.141

Gnomad FIN exome AF: 0.0836

Gnomad NFE exome AF: 0.155

Gnomad OTH exome AF: 0.198

GnomAD4 exome AF: 0.179 AC: 54474 AN: 303522 Hom.: 5541 Cov.: 0 AF XY: 0.189 AC XY: 32751 AN XY: 172892

African (AFR) AF: 0.196 AC: 1685 AN: 8596

American (AMR) AF: 0.182 AC: 4964 AN: 27284

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 2702 AN: 10790

East Asian (EAS) AF: 0.138 AC: 1272 AN: 9218

South Asian (SAS) AF: 0.272 AC: 16232 AN: 59698

European-Finnish (FIN) AF: 0.0891 AC: 1140 AN: 12798

Middle Eastern (MID) AF: 0.326 AC: 648 AN: 1986

European-Non Finnish (NFE) AF: 0.146 AC: 23293 AN: 158998

Other (OTH) AF: 0.179 AC: 2538 AN: 14154

GnomAD4 genome AF: 0.167 AC: 25447 AN: 152178 Hom.: 2350 Cov.: 32 AF XY: 0.167 AC XY: 12420 AN XY: 74406

African (AFR) AF: 0.194 AC: 8044 AN: 41510

American (AMR) AF: 0.192 AC: 2930 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 868 AN: 3472

East Asian (EAS) AF: 0.142 AC: 735 AN: 5166

South Asian (SAS) AF: 0.285 AC: 1372 AN: 4822

European-Finnish (FIN) AF: 0.0906 AC: 961 AN: 10604

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9955 AN: 68006

Other (OTH) AF: 0.187 AC: 394 AN: 2110

Alfa AF: 0.156 Hom.: 8340

Bravo AF: 0.172

Asia WGS AF: 0.229 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
DANN	Benign	0.85
PhyloP100		0.28
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Other links and lift over

dbSNP: rs2277862; hg19: chr20-34152782; COSMIC: COSV53413602;