rs10906723

chr10-14637053-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107B	NM_031453.4	c.469+30581C>T		intron_variant		ENST00000181796.7
FAM107B	NM_001282695.2	c.-123+30581C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7	c.469+30581C>T		intron_variant		2	NM_031453.4
FAM107B	ENST00000487335.5	c.469+30581C>T		intron_variant, NMD_transcript_variant		1

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

Gnomad4 AFR AF: 0.828

Gnomad4 AMR AF: 0.733

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.894

Gnomad4 FIN AF: 0.945

Gnomad4 NFE AF: 0.892

Gnomad4 OTH AF: 0.874

Alfa AF: 0.875 Hom.: 7253

Bravo AF: 0.848

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.056
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10906723; hg19: chr10-14679052;