chr22-39999080-T-C

Variant names:

• chr22-39999080-T-C
• rs3021274
• ENST00000488874.1:n.516T>C

Variant summary

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

The ENST00000488874.1(FAM83F):​n.516T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,112 control chromosomes in the GnomAD database, including 24,996 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 0.56 (24993 hom., cov: 33)
  • Exomes 𝑓: 0.54 (3 hom.)
• Consequence: FAM83F ENST00000488874.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 7 publications found

Genes affected

FAM83F (HGNC:25148): (family with sequence similarity 83 member F) Predicted to enable protein kinase binding activity. Predicted to be involved in signal transduction. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488874.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM83F	NM_138435.4	MANE Select	c.489+3549T>C		intron	N/A	NP_612444.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM83F	ENST00000488874.1	TSL:1	n.516T>C		non_coding_transcript_exon	Exon 3 of 3
	FAM83F	ENST00000333407.11	TSL:1 MANE Select	c.489+3549T>C		intron	N/A	ENSP00000330432.5

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85605 AN: 151968 Hom.: 24954 Cov.: 33

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.523

GnomAD4 exome AF: 0.542 AC: 13 AN: 24 Hom.: 3 Cov.: 0 AF XY: 0.417 AC XY: 5 AN XY: 12

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 9 AN: 18

Other (OTH) AF: 0.750 AC: 3 AN: 4

GnomAD4 genome AF: 0.563 AC: 85697 AN: 152088 Hom.: 24993 Cov.: 33 AF XY: 0.556 AC XY: 41343 AN XY: 74334

African (AFR) AF: 0.672 AC: 27886 AN: 41492

American (AMR) AF: 0.392 AC: 5993 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1941 AN: 3472

East Asian (EAS) AF: 0.230 AC: 1190 AN: 5180

South Asian (SAS) AF: 0.615 AC: 2967 AN: 4824

European-Finnish (FIN) AF: 0.510 AC: 5390 AN: 10566

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38627 AN: 67962

Other (OTH) AF: 0.522 AC: 1101 AN: 2110

Alfa AF: 0.558 Hom.: 58693

Bravo AF: 0.553

Asia WGS AF: 0.449 AC: 1564 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.28
DANN	Benign	0.40
PhyloP100		-1.1
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: rs3021274; hg19: chr22-40395084;