rs3915080

Variant names:

• chr3-22670018-A-G
• rs3915080
• ENST00000448148.1:n.*183T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-22670018-A-G
• chr3-22670018-A-T

Variant summary

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

The ENST00000448148.1(FCRL4P1):​n.*183T>C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 152,006 control chromosomes in the GnomAD database, including 28,277 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 0.61 (28277 hom., cov: 32)
• Consequence: FCRL4P1 ENST00000448148.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.604
• Publications: 1 publications found

Genes affected

FCRL4P1 (HGNC:56400): (FCRL4 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 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
FCRL4P1	ENST00000448148.1	n.*183T>C		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92494 AN: 151888 Hom.: 28279 Cov.: 32

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.609 AC: 92531 AN: 152006 Hom.: 28277 Cov.: 32 AF XY: 0.608 AC XY: 45163 AN XY: 74282

African (AFR) AF: 0.597 AC: 24767 AN: 41464

American (AMR) AF: 0.619 AC: 9460 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1839 AN: 3462

East Asian (EAS) AF: 0.610 AC: 3148 AN: 5158

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4818

European-Finnish (FIN) AF: 0.554 AC: 5843 AN: 10550

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42164 AN: 67966

Other (OTH) AF: 0.602 AC: 1268 AN: 2108

Alfa AF: 0.616 Hom.: 13587

Bravo AF: 0.611

Asia WGS AF: 0.615 AC: 2140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs3915080; hg19: chr3-22711509;