rs1538972

Variant names:

• chr1-161706767-G-A
• rs1538972
• ENST00000367959.6:c.-447G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-161706767-G-A
• chr1-161706767-G-T

Variant summary

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

The ENST00000367959.6(FCRLA):​c.-447G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.836 in 152,178 control chromosomes in the GnomAD database, including 53,451 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 0.84 (53451 hom., cov: 31)
• Consequence: FCRLA ENST00000367959.6 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.947 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FCRLA	ENST00000367959.6	c.-447G>A		upstream_gene_variant		1		ENSP00000356936.2
FCRLA	ENST00000546024.5	c.-447G>A		upstream_gene_variant		1		ENSP00000439838.1
FCRLA	ENST00000540521.5	c.-447G>A		upstream_gene_variant		1		ENSP00000442870.1

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127190 AN: 152060 Hom.: 53417 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.970

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.891

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.836 AC: 127275 AN: 152178 Hom.: 53451 Cov.: 31 AF XY: 0.840 AC XY: 62487 AN XY: 74396

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.897

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.891

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.868

Alfa AF: 0.843 Hom.: 73545

Bravo AF: 0.834

Asia WGS AF: 0.907 AC: 3155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.2
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1538972; hg19: chr1-161676557;