rs16898095

chr8-123181283-T-C

Variant summary

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

The ENST00000518448.5(FAM83A):c.-831-743T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.111 in 152,140 control chromosomes in the GnomAD database, including 1,062 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 0.11 (1062 hom., cov: 32)
• Consequence: FAM83A ENST00000518448.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.699

Genes affected

FAM83A (HGNC:28210): (family with sequence similarity 83 member A) Enables identical protein binding activity; phosphatidylinositol 3-kinase regulatory subunit binding activity; and protein kinase binding activity. Involved in cell population proliferation and epidermal growth factor receptor signaling pathway. Predicted to be located in cytoplasm. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM83A	NM_032899.6	c.-831-743T>C		intron_variant
FAM83A	NM_207006.3	c.-831-743T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM83A	ENST00000518448.5	c.-831-743T>C		intron_variant		1		P1
FAM83A	ENST00000536633.2	c.-831-743T>C		intron_variant		2
FAM83A	ENST00000520541.5	n.356+1054T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16815 AN: 152022 Hom.: 1053 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0648

Gnomad AMR AF: 0.0744

Gnomad ASJ AF: 0.0726

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00994

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0935

Gnomad OTH AF: 0.0923

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

GnomAD4 genome AF: 0.111 AC: 16850 AN: 152140 Hom.: 1062 Cov.: 32 AF XY: 0.109 AC XY: 8095 AN XY: 74380

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0726

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00995

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.0935

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.0914 Hom.: 861

Bravo AF: 0.110

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	8.7
Dann	Benign	0.31

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: rs16898095; hg19: chr8-124193523;