rs9310704

Variant names:

• chr3-22669955-G-A
• rs9310704
• ENST00000448148.1:n.*246C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-22669955-G-A
• chr3-22669955-G-C

Variant summary

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

The ENST00000448148.1(FCRL4P1):​n.*246C>T 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 152,018 control chromosomes in the GnomAD database, including 28,270 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 (28270 hom., cov: 32)
• Consequence: FCRL4P1 ENST00000448148.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.576
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 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.*246C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.609 AC: 92488 AN: 151900 Hom.: 28272 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.681

Gnomad AMR AF: 0.620

Gnomad ASJ AF: 0.530

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.564

Gnomad NFE AF: 0.621

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: 92525 AN: 152018 Hom.: 28270 Cov.: 32 AF XY: 0.608 AC XY: 45177 AN XY: 74314

African (AFR) AF: 0.597 AC: 24724 AN: 41438

American (AMR) AF: 0.619 AC: 9463 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.530 AC: 1836 AN: 3464

East Asian (EAS) AF: 0.610 AC: 3150 AN: 5164

South Asian (SAS) AF: 0.677 AC: 3257 AN: 4814

European-Finnish (FIN) AF: 0.555 AC: 5864 AN: 10574

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.620 AC: 42174 AN: 67972

Other (OTH) AF: 0.601 AC: 1270 AN: 2112

Alfa AF: 0.615 Hom.: 14291

Bravo AF: 0.610

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.44
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9310704; hg19: chr3-22711446;