chr10-14546602-T-G

Variant names:

• chr10-14546602-T-G
• rs7079377
• NM_031453.4:c.470-16087A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031453.4(FAM107B):​c.470-16087A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.801 in 152,142 control chromosomes in the GnomAD database, including 49,329 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 0.80 (49329 hom., cov: 32)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.866 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.470-16087A>C		intron	N/A	NP_113641.2
	FAM107B	NM_001282695.2		c.-57+6720A>C		intron	N/A	NP_001269624.1
	FAM107B	NM_001282696.2		c.-57+6720A>C		intron	N/A	NP_001269625.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM107B	ENST00000181796.7	TSL:2 MANE Select	c.470-16087A>C		intron	N/A	ENSP00000181796.2
	FAM107B	ENST00000378467.8	TSL:1	c.-57+6720A>C		intron	N/A	ENSP00000367728.4
	FAM107B	ENST00000378470.5	TSL:1	c.-57+1838A>C		intron	N/A	ENSP00000367731.1

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121736 AN: 152024 Hom.: 49286 Cov.: 32

Gnomad AFR AF: 0.676

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.801 AC: 121833 AN: 152142 Hom.: 49329 Cov.: 32 AF XY: 0.803 AC XY: 59744 AN XY: 74402

African (AFR) AF: 0.677 AC: 28045 AN: 41452

American (AMR) AF: 0.738 AC: 11287 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3167 AN: 3472

East Asian (EAS) AF: 0.887 AC: 4589 AN: 5172

South Asian (SAS) AF: 0.882 AC: 4255 AN: 4822

European-Finnish (FIN) AF: 0.867 AC: 9195 AN: 10606

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58556 AN: 68004

Other (OTH) AF: 0.813 AC: 1717 AN: 2112

Alfa AF: 0.827 Hom.: 15023

Bravo AF: 0.783

Asia WGS AF: 0.871 AC: 3030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.69
DANN	Benign	0.27
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs7079377; hg19: chr10-14588601;