rs10906723

Variant names:

• chr10-14637053-G-A
• rs10906723
• NM_031453.4:c.469+30581C>T

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+30581C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.865 in 152,168 control chromosomes in the GnomAD database, including 57,283 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 0.87 (57283 hom., cov: 31)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• 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]

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 (EAS) allele frequency at 95% confidence interval = 0.929 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	NM_031453.4	MANE Select	c.469+30581C>T		intron	N/A	NP_113641.2
	FAM107B	NM_001282695.2		c.-123+30581C>T		intron	N/A	NP_001269624.1	Q9H098-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	ENST00000181796.7	TSL:2 MANE Select	c.469+30581C>T		intron	N/A	ENSP00000181796.2	Q9H098-2
	FAM107B	ENST00000487335.5	TSL:1	n.469+30581C>T		intron	N/A	ENSP00000420273.1	F8WDH7

Frequencies

GnomAD3 genomes AF: 0.865 AC: 131578 AN: 152050 Hom.: 57240 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.945

Gnomad AMR AF: 0.733

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.894

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.872

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

GnomAD4 genome AF: 0.865 AC: 131674 AN: 152168 Hom.: 57283 Cov.: 31 AF XY: 0.866 AC XY: 64440 AN XY: 74404

African (AFR) AF: 0.828 AC: 34361 AN: 41484

American (AMR) AF: 0.733 AC: 11191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3186 AN: 3470

East Asian (EAS) AF: 0.951 AC: 4925 AN: 5180

South Asian (SAS) AF: 0.894 AC: 4317 AN: 4828

European-Finnish (FIN) AF: 0.945 AC: 10030 AN: 10612

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60684 AN: 68004

Other (OTH) AF: 0.874 AC: 1845 AN: 2112

Alfa AF: 0.873 Hom.: 7524

Bravo AF: 0.848

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.056
DANN	Benign	0.17
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: rs10906723; hg19: chr10-14679052;