chr22-40002841-A-G

Variant names:

• chr22-40002841-A-G
• rs739145
• NM_138435.4:c.489+7310A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138435.4. 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+7310A>G		intron	N/A	NP_612444.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM83F	ENST00000333407.11	TSL:1 MANE Select	c.489+7310A>G		intron	N/A	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

African (AFR) AF: 0.672 AC: 27886 AN: 41476

American (AMR) AF: 0.397 AC: 6065 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.572 AC: 1986 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1196 AN: 5170

South Asian (SAS) AF: 0.643 AC: 3099 AN: 4822

European-Finnish (FIN) AF: 0.558 AC: 5885 AN: 10556

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40329 AN: 67966

Other (OTH) AF: 0.530 AC: 1116 AN: 2106

Alfa AF: 0.536 Hom.: 3464

Bravo AF: 0.574

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.22
PhyloP100		0.084
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: rs739145; hg19: chr22-40398845;