8-123908962-C-T

Variant summary

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

The NM_001039112.2(FER1L6):c.-7-47030C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.314 in 151,972 control chromosomes in the GnomAD database, including 8,256 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 0.31 (8256 hom., cov: 32)
• Consequence: FER1L6 NM_001039112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

FER1L6 (HGNC:28065): (fer-1 like family member 6) Predicted to enable metal ion binding activity. Predicted to be involved in plasma membrane organization. Predicted to act upstream of or within response to bacterium. 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FER1L6	NM_001039112.2	c.-7-47030C>T		intron_variant		ENST00000522917.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FER1L6	ENST00000522917.5	c.-7-47030C>T		intron_variant		1	NM_001039112.2	P1

Frequencies

GnomAD3 genomes AF: 0.314 AC: 47728 AN: 151854 Hom.: 8252 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.473

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.314 AC: 47752 AN: 151972 Hom.: 8256 Cov.: 32 AF XY: 0.306 AC XY: 22745 AN XY: 74248

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.443

Gnomad4 EAS AF: 0.171

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.345

Alfa AF: 0.361 Hom.: 5551

Bravo AF: 0.315

Asia WGS AF: 0.284 AC: 992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.3
Dann	Benign	0.69

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12548182; hg19: chr8-124921202;