rs739145

Positions:

• chr22-40002841-A-G
• chr22-40002841-A-T

Variant summary

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

The NM_138435.4(FAM83F):​c.489+7310A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 152,042 control chromosomes in the GnomAD database, including 26,459 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 0.58 (26459 hom., cov: 31)
• Consequence: FAM83F NM_138435.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0840

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM83F	NM_138435.4	c.489+7310A>G		intron_variant		ENST00000333407.11	NP_612444.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM83F	ENST00000333407.11	c.489+7310A>G		intron_variant		1	NM_138435.4	ENSP00000330432.5

Frequencies

GnomAD3 genomes AF: 0.580 AC: 88110 AN: 151924 Hom.: 26439 Cov.: 31

Gnomad AFR AF: 0.673

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.398

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.533

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

GnomAD4 genome AF: 0.580 AC: 88171 AN: 152042 Hom.: 26459 Cov.: 31 AF XY: 0.573 AC XY: 42592 AN XY: 74314

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.397

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.231

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.530

Alfa AF: 0.536 Hom.: 3464

Bravo AF: 0.574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.22

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: rs739145; hg19: chr22-40398845;