NM_001039112.2:c.-29G>A

Variant names:

• chr8-123852164-G-A
• rs1897318
• NM_001039112.2:c.-29G>A

Variant summary

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

The NM_001039112.2(FER1L6):​c.-29G>A variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,134 control chromosomes in the GnomAD database, including 12,529 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 0.39 (12524 hom., cov: 32)
  • Exomes 𝑓: 0.55 (5 hom.)
• Consequence: FER1L6 NM_001039112.2 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039112.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FER1L6	NM_001039112.2	MANE Select	c.-29G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 41	NP_001034201.2
	FER1L6	NM_001039112.2	MANE Select	c.-29G>A		5_prime_UTR	Exon 1 of 41	NP_001034201.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FER1L6	ENST00000522917.5	TSL:1 MANE Select	c.-29G>A		5_prime_UTR_premature_start_codon_gain	Exon 1 of 41	ENSP00000428280.1
	FER1L6	ENST00000522917.5	TSL:1 MANE Select	c.-29G>A		5_prime_UTR	Exon 1 of 41	ENSP00000428280.1

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59895 AN: 151974 Hom.: 12525 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.465

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.391

GnomAD4 exome AF: 0.548 AC: 23 AN: 42 Hom.: 5 Cov.: 0 AF XY: 0.563 AC XY: 18 AN XY: 32

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.611 AC: 22 AN: 36

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.394 AC: 59903 AN: 152092 Hom.: 12524 Cov.: 32 AF XY: 0.388 AC XY: 28813 AN XY: 74350

African (AFR) AF: 0.337 AC: 13968 AN: 41484

American (AMR) AF: 0.294 AC: 4489 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1458 AN: 3468

East Asian (EAS) AF: 0.123 AC: 638 AN: 5176

South Asian (SAS) AF: 0.242 AC: 1166 AN: 4820

European-Finnish (FIN) AF: 0.465 AC: 4920 AN: 10574

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.468 AC: 31790 AN: 67976

Other (OTH) AF: 0.391 AC: 827 AN: 2114

Alfa AF: 0.430 Hom.: 23860

Bravo AF: 0.381

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.59
PromoterAI		-0.012	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1897318; hg19: chr8-124864404;