rs7249320

Variant names:

• chr19-7698159-C-A
• rs7249320
• NM_001220500.2:c.190+197G>T

Your query was ambiguous. Multiple possible variants found:

• chr19-7698159-C-A
• chr19-7698159-C-T

Variant summary

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

The NM_001220500.2(FCER2):​c.190+197G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 152,064 control chromosomes in the GnomAD database, including 7,086 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 0.29 (7086 hom., cov: 31)
• Consequence: FCER2 NM_001220500.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 15 publications found

Genes affected

FCER2 (HGNC:3612): (Fc epsilon receptor II) The protein encoded by this gene is a B-cell specific antigen, and a low-affinity receptor for IgE. It has essential roles in B cell growth and differentiation, and the regulation of IgE production. This protein also exists as a soluble secreted form, then functioning as a potent mitogenic growth factor. Alternatively spliced transcript variants encoding different isoforms have been described for this gene.[provided by RefSeq, Jul 2011]

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 (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FCER2	NM_001220500.2	c.190+197G>T		intron_variant	Intron 4 of 10	ENST00000597921.6	NP_001207429.1
FCER2	NM_002002.5	c.190+197G>T		intron_variant	Intron 4 of 10		NP_001993.2
FCER2	NM_001207019.3	c.187+197G>T		intron_variant	Intron 3 of 9		NP_001193948.2
FCER2	XM_005272462.5	c.190+197G>T		intron_variant	Intron 4 of 10		XP_005272519.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCER2	ENST00000597921.6	c.190+197G>T		intron_variant	Intron 4 of 10	1	NM_001220500.2	ENSP00000471974.1

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44016 AN: 151946 Hom.: 7077 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.242

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.290 AC: 44056 AN: 152064 Hom.: 7086 Cov.: 31 AF XY: 0.287 AC XY: 21345 AN XY: 74322

African (AFR) AF: 0.438 AC: 18144 AN: 41468

American (AMR) AF: 0.216 AC: 3299 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.242 AC: 838 AN: 3464

East Asian (EAS) AF: 0.151 AC: 781 AN: 5170

South Asian (SAS) AF: 0.342 AC: 1650 AN: 4822

European-Finnish (FIN) AF: 0.203 AC: 2149 AN: 10574

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.238 AC: 16199 AN: 67972

Other (OTH) AF: 0.279 AC: 590 AN: 2114

Alfa AF: 0.215 Hom.: 1438

Bravo AF: 0.294

Asia WGS AF: 0.252 AC: 877 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	0.97
DANN	Benign	0.49
PhyloP100		-0.77
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: rs7249320; hg19: chr19-7763045; COSMIC: COSV107410272;