chr8-124030312-G-C

Variant names:

• chr8-124030312-G-C
• rs9297682
• NM_001039112.2:c.2287-4965G>C

Variant summary

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

The NM_001039112.2(FER1L6):​c.2287-4965G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,044 control chromosomes in the GnomAD database, including 8,023 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 0.32 (8023 hom., cov: 31)
• Consequence: FER1L6 NM_001039112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.859
• Publications: 4 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]

FER1L6-AS1 (HGNC:26652): (FER1L6 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FER1L6	NM_001039112.2	c.2287-4965G>C		intron_variant	Intron 18 of 40	ENST00000522917.5	NP_001034201.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FER1L6	ENST00000522917.5	c.2287-4965G>C		intron_variant	Intron 18 of 40	1	NM_001039112.2	ENSP00000428280.1
FER1L6-AS1	ENST00000518567.1	n.157+10314C>G		intron_variant	Intron 1 of 5	2

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48372 AN: 151924 Hom.: 8007 Cov.: 31

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.318 AC: 48421 AN: 152044 Hom.: 8023 Cov.: 31 AF XY: 0.322 AC XY: 23895 AN XY: 74304

African (AFR) AF: 0.229 AC: 9475 AN: 41464

American (AMR) AF: 0.340 AC: 5190 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1136 AN: 3470

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5172

South Asian (SAS) AF: 0.359 AC: 1724 AN: 4808

European-Finnish (FIN) AF: 0.394 AC: 4168 AN: 10568

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.358 AC: 24309 AN: 67978

Other (OTH) AF: 0.336 AC: 708 AN: 2110

Alfa AF: 0.331 Hom.: 1088

Bravo AF: 0.308

Asia WGS AF: 0.320 AC: 1117 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.30
PhyloP100		0.86
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9297682; hg19: chr8-125042552;