8-124096736-T-C

Variant names:

• chr8-124096736-T-C
• rs4870888
• NM_001039112.2:c.4696-535T>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.4696-535T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 151,994 control chromosomes in the GnomAD database, including 12,090 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 (12090 hom., cov: 31)
• Consequence: FER1L6 NM_001039112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• 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-AS2 (HGNC:26534): (FER1L6 antisense RNA 2)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FER1L6	NM_001039112.2	c.4696-535T>C		intron_variant	Intron 35 of 40	ENST00000522917.5	NP_001034201.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FER1L6	ENST00000522917.5	c.4696-535T>C		intron_variant	Intron 35 of 40	1	NM_001039112.2	ENSP00000428280.1
FER1L6-AS2	ENST00000520031.1	n.96-35944A>G		intron_variant	Intron 1 of 4	2
FER1L6-AS2	ENST00000661827.1	n.25-35944A>G		intron_variant	Intron 1 of 1
FER1L6-AS2	ENST00000669903.2	n.103-35944A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.389 AC: 59012 AN: 151876 Hom.: 12098 Cov.: 31

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.388 AC: 59018 AN: 151994 Hom.: 12090 Cov.: 31 AF XY: 0.387 AC XY: 28770 AN XY: 74298

African (AFR) AF: 0.254 AC: 10515 AN: 41420

American (AMR) AF: 0.373 AC: 5692 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1695 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1642 AN: 5176

South Asian (SAS) AF: 0.509 AC: 2453 AN: 4816

European-Finnish (FIN) AF: 0.412 AC: 4351 AN: 10568

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.460 AC: 31282 AN: 67966

Other (OTH) AF: 0.415 AC: 878 AN: 2116

Alfa AF: 0.434 Hom.: 46681

Bravo AF: 0.379

Asia WGS AF: 0.395 AC: 1377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs4870888; hg19: chr8-125108977;