rs9692809

Variant names:

• chr8-7331836-C-T
• rs9692809
• ENST00000606573.1:n.704-6421G>A

Variant summary

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

The ENST00000606573.1(FAM66B):​n.704-6421G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.12 (1651 hom., cov: 13)
• Consequence: FAM66B ENST00000606573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 6 publications found

Genes affected

FAM66B (HGNC:28890): (family with sequence similarity 66 member B)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM66B	NR_027423.2	n.618-6638G>A		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM66B	ENST00000606573.1	n.704-6421G>A		intron_variant	Intron 2 of 5	1
FAM66B	ENST00000529456.2	n.610-6638G>A		intron_variant	Intron 2 of 6	2
FAM66B	ENST00000653873.2	n.596-6638G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.125 AC: 13076 AN: 104866 Hom.: 1645 Cov.: 13

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0829

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.0851

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.126

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

GnomAD4 genome AF: 0.125 AC: 13090 AN: 104894 Hom.: 1651 Cov.: 13 AF XY: 0.121 AC XY: 6030 AN XY: 49942

African (AFR) AF: 0.279 AC: 3652 AN: 13094

American (AMR) AF: 0.0827 AC: 928 AN: 11226

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 420 AN: 2972

East Asian (EAS) AF: 0.0751 AC: 324 AN: 4314

South Asian (SAS) AF: 0.0848 AC: 274 AN: 3230

European-Finnish (FIN) AF: 0.0873 AC: 711 AN: 8142

Middle Eastern (MID) AF: 0.193 AC: 44 AN: 228

European-Non Finnish (NFE) AF: 0.108 AC: 6445 AN: 59438

Other (OTH) AF: 0.132 AC: 185 AN: 1400

Alfa AF: 0.116 Hom.: 532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.66
DANN	Benign	0.73
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs9692809; hg19: chr8-7189358;