rs6911198

Variant names:

• chr6-54856819-G-A
• rs6911198
• NM_001010872.3:c.-61+9993G>A

Variant summary

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

The NM_001010872.3(FAM83B):​c.-61+9993G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 151,854 control chromosomes in the GnomAD database, including 16,452 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 0.46 (16452 hom., cov: 31)
• Consequence: FAM83B NM_001010872.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0220
• Publications: 4 publications found

Genes affected

FAM83B (HGNC:21357): (family with sequence similarity 83 member B) Enables epidermal growth factor receptor binding activity; phosphatidylinositol 3-kinase binding activity; and protein kinase binding activity. Involved in cell population proliferation and epidermal growth factor receptor signaling pathway. Located in cytoplasm and membrane. [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 (NFE) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM83B	NM_001010872.3	c.-61+9993G>A		intron_variant	Intron 1 of 4	ENST00000306858.8	NP_001010872.1
FAM83B	XM_006715022.4	c.-61+10104G>A		intron_variant	Intron 1 of 4		XP_006715085.1
FAM83B	XM_011514394.3	c.-61+7153G>A		intron_variant	Intron 1 of 4		XP_011512696.1
FAM83B	XM_017010478.2	c.-61+10415G>A		intron_variant	Intron 1 of 4		XP_016865967.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM83B	ENST00000306858.8	c.-61+9993G>A		intron_variant	Intron 1 of 4	1	NM_001010872.3	ENSP00000304078.7

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69424 AN: 151736 Hom.: 16440 Cov.: 31

Gnomad AFR AF: 0.435

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.461

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.510

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.457 AC: 69467 AN: 151854 Hom.: 16452 Cov.: 31 AF XY: 0.453 AC XY: 33627 AN XY: 74196

African (AFR) AF: 0.435 AC: 18003 AN: 41386

American (AMR) AF: 0.344 AC: 5251 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.461 AC: 1599 AN: 3470

East Asian (EAS) AF: 0.186 AC: 962 AN: 5162

South Asian (SAS) AF: 0.480 AC: 2309 AN: 4810

European-Finnish (FIN) AF: 0.473 AC: 4965 AN: 10498

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.510 AC: 34627 AN: 67932

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.489 Hom.: 78456

Bravo AF: 0.444

Asia WGS AF: 0.326 AC: 1133 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.41
PhyloP100		0.022
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: rs6911198; hg19: chr6-54721617;