rs6088887

chr20-35583402-G-A

Variant summary

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

The NR_119376.1(FER1L4):n.3073-140C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 372,570 control chromosomes in the GnomAD database, including 8,173 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 (2990 hom., cov: 32)
  • Exomes 𝑓: 0.21 (5183 hom.)
• Consequence: FER1L4 NR_119376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.153

Genes affected

(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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FER1L4	NR_119376.1	n.3073-140C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000430275.6	n.2948-140C>T		intron_variant, non_coding_transcript_variant		5
FER1L4	ENST00000615531.4	n.3005-140C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29005 AN: 151828 Hom.: 2989 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0904

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.205 AC: 45279 AN: 220624 Hom.: 5183 AF XY: 0.216 AC XY: 26354 AN XY: 122234

Gnomad4 AFR exome AF: 0.195

Gnomad4 AMR exome AF: 0.159

Gnomad4 ASJ exome AF: 0.293

Gnomad4 EAS exome AF: 0.0847

Gnomad4 SAS exome AF: 0.281

Gnomad4 FIN exome AF: 0.141

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.204

GnomAD4 genome AF: 0.191 AC: 29008 AN: 151946 Hom.: 2990 Cov.: 32 AF XY: 0.189 AC XY: 14030 AN XY: 74282

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0908

Gnomad4 SAS AF: 0.286

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.219

Alfa AF: 0.201 Hom.: 6433

Bravo AF: 0.190

Asia WGS AF: 0.203 AC: 705 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.86
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6088887; hg19: chr20-34171324;