chr1-161708017-C-T

Position:

• chr1-161708017-C-T

Variant summary

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

The NM_032738.4(FCRLA):​c.79+674C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.058 in 152,184 control chromosomes in the GnomAD database, including 700 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 0.058 (700 hom., cov: 32)
• Consequence: FCRLA NM_032738.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.726

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FCRLA	NM_032738.4	c.79+674C>T		intron_variant		ENST00000236938.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FCRLA	ENST00000236938.12	c.79+674C>T		intron_variant		1	NM_032738.4	A2

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8811 AN: 152066 Hom.: 700 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0281

Gnomad ASJ AF: 0.0161

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.00980

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0226

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0580 AC: 8820 AN: 152184 Hom.: 700 Cov.: 32 AF XY: 0.0571 AC XY: 4246 AN XY: 74406

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.0280

Gnomad4 ASJ AF: 0.0161

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.0290

Gnomad4 FIN AF: 0.00980

Gnomad4 NFE AF: 0.0226

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0304 Hom.: 70

Bravo AF: 0.0651

Asia WGS AF: 0.157 AC: 548 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.51

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: rs1954174; hg19: chr1-161677807;