rs6119625

Positions:

• chr20-35572533-A-G

Variant summary

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

The NR_119376.1(FER1L4):​n.4393+3634T>C 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 0.167 in 152,114 control chromosomes in the GnomAD database, including 2,357 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 (2357 hom., cov: 32)
• Consequence: FER1L4 NR_119376.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FER1L4	NR_119376.1	n.4393+3634T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FER1L4	ENST00000615531.4	n.4381+3634T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25456 AN: 151996 Hom.: 2356 Cov.: 32

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.284

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.148

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.167 AC: 25473 AN: 152114 Hom.: 2357 Cov.: 32 AF XY: 0.167 AC XY: 12434 AN XY: 74384

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.253

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.148

Gnomad4 OTH AF: 0.188

Alfa AF: 0.164 Hom.: 384

Bravo AF: 0.172

Asia WGS AF: 0.233 AC: 811 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.9
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6119625; hg19: chr20-34160455;