rs7922166

Positions:

• chr10-14656550-T-A
• chr10-14656550-T-G

Variant summary

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

The NM_031453.4(FAM107B):​c.469+11084A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.935 in 152,254 control chromosomes in the GnomAD database, including 66,799 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 0.94 (66799 hom., cov: 31)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

FAM107B (HGNC:23726): (family with sequence similarity 107 member B) Predicted to act upstream of or within sensory perception of sound. [provided by Alliance of Genome Resources, Apr 2022]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM107B	NM_031453.4	c.469+11084A>T		intron_variant		ENST00000181796.7	NP_113641.2
LOC105376429	XR_930691.4	n.412+326T>A		intron_variant, non_coding_transcript_variant
FAM107B	NM_001282695.2	c.-123+11084A>T		intron_variant			NP_001269624.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM107B	ENST00000181796.7	c.469+11084A>T		intron_variant		2	NM_031453.4	ENSP00000181796
FAM107B	ENST00000487335.5	c.469+11084A>T		intron_variant, NMD_transcript_variant		1		ENSP00000420273
	ENST00000443282.1	n.225+2584T>A		intron_variant, non_coding_transcript_variant		3
	ENST00000647862.1	n.388+326T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.935 AC: 142256 AN: 152136 Hom.: 66743 Cov.: 31

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.874

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.704

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.938

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

GnomAD4 genome AF: 0.935 AC: 142368 AN: 152254 Hom.: 66799 Cov.: 31 AF XY: 0.933 AC XY: 69433 AN XY: 74450

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.874

Gnomad4 ASJ AF: 0.929

Gnomad4 EAS AF: 0.704

Gnomad4 SAS AF: 0.883

Gnomad4 FIN AF: 0.965

Gnomad4 NFE AF: 0.946

Gnomad4 OTH AF: 0.936

Alfa AF: 0.949 Hom.: 3202

Bravo AF: 0.927

Asia WGS AF: 0.775 AC: 2696 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7922166; hg19: chr10-14698549;