8-123887942-C-T

Variant names:

• chr8-123887942-C-T
• rs11787464
• NM_001039112.2:c.-8+35757C>T

Variant summary

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

The NM_001039112.2(FER1L6):​c.-8+35757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 151,906 control chromosomes in the GnomAD database, including 7,901 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 0.30 (7901 hom., cov: 31)
• Consequence: FER1L6 NM_001039112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• 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=-0.79).
• 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 rank	MANE	Protein	UniProt
FER1L6	NM_001039112.2	c.-8+35757C>T		intron_variant	Intron 1 of 40	ENST00000522917.5	NP_001034201.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FER1L6	ENST00000522917.5	c.-8+35757C>T		intron_variant	Intron 1 of 40	1	NM_001039112.2	ENSP00000428280.1

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46044 AN: 151792 Hom.: 7901 Cov.: 31

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.303 AC: 46055 AN: 151906 Hom.: 7901 Cov.: 31 AF XY: 0.295 AC XY: 21913 AN XY: 74232

African (AFR) AF: 0.156 AC: 6478 AN: 41446

American (AMR) AF: 0.315 AC: 4802 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1523 AN: 3460

East Asian (EAS) AF: 0.165 AC: 853 AN: 5164

South Asian (SAS) AF: 0.366 AC: 1758 AN: 4806

European-Finnish (FIN) AF: 0.254 AC: 2678 AN: 10532

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26696 AN: 67922

Other (OTH) AF: 0.338 AC: 715 AN: 2114

Alfa AF: 0.376 Hom.: 5844

Bravo AF: 0.304

Asia WGS AF: 0.263 AC: 919 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	4.9
DANN	Benign	0.68
PhyloP100		0.21
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: rs11787464; hg19: chr8-124900182;