NM_001039112.2:c.-7-39970C>T

Variant names:

• chr8-123916022-C-T
• rs16893054
• NM_001039112.2:c.-7-39970C>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.-7-39970C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 151,942 control chromosomes in the GnomAD database, including 9,100 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 0.34 (9100 hom., cov: 31)
• Consequence: FER1L6 NM_001039112.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.546
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FER1L6	NM_001039112.2	c.-7-39970C>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.-7-39970C>T		intron_variant	Intron 1 of 40	1	NM_001039112.2	ENSP00000428280.1

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50804 AN: 151824 Hom.: 9065 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.259

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.335 AC: 50902 AN: 151942 Hom.: 9100 Cov.: 31 AF XY: 0.343 AC XY: 25435 AN XY: 74254

African (AFR) AF: 0.436 AC: 18058 AN: 41426

American (AMR) AF: 0.327 AC: 4999 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.259 AC: 899 AN: 3470

East Asian (EAS) AF: 0.445 AC: 2286 AN: 5138

South Asian (SAS) AF: 0.422 AC: 2027 AN: 4808

European-Finnish (FIN) AF: 0.383 AC: 4047 AN: 10556

Middle Eastern (MID) AF: 0.154 AC: 45 AN: 292

European-Non Finnish (NFE) AF: 0.260 AC: 17652 AN: 67960

Other (OTH) AF: 0.284 AC: 600 AN: 2110

Alfa AF: 0.216 Hom.: 708

Bravo AF: 0.332

Asia WGS AF: 0.427 AC: 1480 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.55
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: rs16893054; hg19: chr8-124928262;