chr1-161217875-C-T

Variant names:

• chr1-161217875-C-T
• rs2070902
• NM_004106.2:c.50-111C>T

Variant summary

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

The NM_004106.2(FCER1G):​c.50-111C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.291 in 738,910 control chromosomes in the GnomAD database, including 33,241 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 0.31 (7602 hom., cov: 31)
  • Exomes 𝑓: 0.29 (25639 hom.)
• Consequence: FCER1G NM_004106.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 40 publications found

Genes affected

FCER1G (HGNC:3611): (Fc epsilon receptor Ig) The high affinity IgE receptor is a key molecule involved in allergic reactions. It is a tetramer composed of 1 alpha, 1 beta, and 2 gamma chains. The gamma chains are also subunits of other Fc receptors. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER1G	NM_004106.2	c.50-111C>T		intron_variant	Intron 1 of 4	ENST00000289902.2	NP_004097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER1G	ENST00000289902.2	c.50-111C>T		intron_variant	Intron 1 of 4	1	NM_004106.2	ENSP00000289902.1
FCER1G	ENST00000367992.7	c.50-111C>T		intron_variant	Intron 1 of 4	3		ENSP00000356971.3
FCER1G	ENST00000490414.1	n.138-366C>T		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46777 AN: 151706 Hom.: 7585 Cov.: 31

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.287

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.323

GnomAD4 exome AF: 0.287 AC: 168406 AN: 587086 Hom.: 25639 AF XY: 0.287 AC XY: 90206 AN XY: 314724

African (AFR) AF: 0.392 AC: 6332 AN: 16168

American (AMR) AF: 0.373 AC: 12668 AN: 34004

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 4578 AN: 16410

East Asian (EAS) AF: 0.450 AC: 16007 AN: 35574

South Asian (SAS) AF: 0.357 AC: 21291 AN: 59642

European-Finnish (FIN) AF: 0.286 AC: 13271 AN: 46380

Middle Eastern (MID) AF: 0.309 AC: 1143 AN: 3694

European-Non Finnish (NFE) AF: 0.244 AC: 84016 AN: 344310

Other (OTH) AF: 0.294 AC: 9100 AN: 30904

GnomAD4 genome AF: 0.309 AC: 46840 AN: 151824 Hom.: 7602 Cov.: 31 AF XY: 0.312 AC XY: 23155 AN XY: 74192

African (AFR) AF: 0.381 AC: 15749 AN: 41332

American (AMR) AF: 0.331 AC: 5048 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.287 AC: 996 AN: 3468

East Asian (EAS) AF: 0.429 AC: 2212 AN: 5158

South Asian (SAS) AF: 0.381 AC: 1835 AN: 4810

European-Finnish (FIN) AF: 0.299 AC: 3154 AN: 10556

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16881 AN: 67918

Other (OTH) AF: 0.328 AC: 693 AN: 2112

Alfa AF: 0.264 Hom.: 8623

Bravo AF: 0.319

Asia WGS AF: 0.414 AC: 1436 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.69
DANN	Benign	0.56
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.11		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: rs2070902; hg19: chr1-161187665; COSMIC: COSV57154356; COSMIC: COSV57154356;