rs1954173

Variant names:

• chr1-161707994-G-A
• rs1954173
• NM_032738.4:c.79+651G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FCRLA	NM_032738.4	c.79+651G>A		intron_variant	Intron 1 of 4	ENST00000236938.12	NP_116127.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRLA	ENST00000236938.12	c.79+651G>A		intron_variant	Intron 1 of 4	1	NM_032738.4	ENSP00000236938.7

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

African (AFR) AF: 0.523 AC: 21680 AN: 41420

American (AMR) AF: 0.527 AC: 8047 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2193 AN: 3470

East Asian (EAS) AF: 0.819 AC: 4240 AN: 5176

South Asian (SAS) AF: 0.524 AC: 2524 AN: 4820

European-Finnish (FIN) AF: 0.661 AC: 6983 AN: 10560

Middle Eastern (MID) AF: 0.562 AC: 163 AN: 290

European-Non Finnish (NFE) AF: 0.625 AC: 42488 AN: 67938

Other (OTH) AF: 0.611 AC: 1290 AN: 2110

Alfa AF: 0.606 Hom.: 14307

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
PhyloP100		-0.29
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: rs1954173; hg19: chr1-161677784;