rs7922166

Variant names:

• chr10-14656550-T-A
• rs7922166
• NM_031453.4:c.469+11084A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

ENSG00000236495 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031453.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	NM_031453.4	MANE Select	c.469+11084A>T		intron	N/A	NP_113641.2
	FAM107B	NM_001282695.2		c.-123+11084A>T		intron	N/A	NP_001269624.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	ENST00000181796.7	TSL:2 MANE Select	c.469+11084A>T		intron	N/A	ENSP00000181796.2
	FAM107B	ENST00000487335.5	TSL:1	n.469+11084A>T		intron	N/A	ENSP00000420273.1
	ENSG00000236495	ENST00000443282.1	TSL:3	n.225+2584T>A		intron	N/A

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

African (AFR) AF: 0.967 AC: 40178 AN: 41546

American (AMR) AF: 0.874 AC: 13372 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3223 AN: 3470

East Asian (EAS) AF: 0.704 AC: 3626 AN: 5154

South Asian (SAS) AF: 0.883 AC: 4259 AN: 4826

European-Finnish (FIN) AF: 0.965 AC: 10238 AN: 10608

Middle Eastern (MID) AF: 0.942 AC: 277 AN: 294

European-Non Finnish (NFE) AF: 0.946 AC: 64331 AN: 68030

Other (OTH) AF: 0.936 AC: 1977 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.050
DANN	Benign	0.50
PhyloP100		-1.1
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: rs7922166; hg19: chr10-14698549;