rs1954173

chr1-161707994-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032738.4(FCRLA):c.79+651G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,952 control chromosomes in the GnomAD database, including 26,978 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 0.59 (26978 hom., cov: 32)
• Consequence: FCRLA NM_032738.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

FCRLA (HGNC:18504): (Fc receptor like A) This gene encodes a protein similar to receptors for the Fc fragment of gamma immunoglobulin (IgG). These receptors, referred to as FCGRs, mediate the destruction of IgG-coated antigens and of cells induced by antibodies. This encoded protein is selectively expressed in B cells, and may be involved in their development. This protein may also be involved in the development of lymphomas. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.799 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRLA	NM_032738.4	c.79+651G>A		intron_variant		ENST00000236938.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRLA	ENST00000236938.12	c.79+651G>A		intron_variant		1	NM_032738.4	A2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 89967 AN: 151834 Hom.: 26962 Cov.: 32

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.437

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.819

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.592 AC: 90006 AN: 151952 Hom.: 26978 Cov.: 32 AF XY: 0.591 AC XY: 43922 AN XY: 74280

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.632

Gnomad4 EAS AF: 0.819

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.611

Alfa AF: 0.604 Hom.: 12807

Bravo AF: 0.582

Asia WGS AF: 0.651 AC: 2264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	1.7
Dann	Benign	0.40

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

Publications

LitVar

Other links and lift over

dbSNP: rs1954173; hg19: chr1-161677784;