rs9692809

Positions:

• chr8-7331836-C-T

Variant summary

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

The NR_027423.2(FAM66B):​n.618-6638G>A variant causes a intron, non coding transcript 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 NR_027423.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
FAM66B	NR_027423.2	n.618-6638G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM66B	ENST00000664195.1	n.614-6638G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.0827

Gnomad4 ASJ AF: 0.141

Gnomad4 EAS AF: 0.0751

Gnomad4 SAS AF: 0.0848

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.132

Alfa AF: 0.118 Hom.: 484

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9692809; hg19: chr8-7189358;