rs1459019

Positions:

• chr10-14670444-A-G

Variant summary

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

The NM_031453.4(FAM107B):​c.412-2753T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,088 control chromosomes in the GnomAD database, including 9,872 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 0.36 (9872 hom., cov: 33)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.623

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM107B	NM_031453.4	c.412-2753T>C		intron_variant		ENST00000181796.7
FAM107B	NM_001282695.2	c.-180-2753T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM107B	ENST00000181796.7	c.412-2753T>C		intron_variant		2	NM_031453.4
FAM107B	ENST00000487335.5	c.412-2753T>C		intron_variant, NMD_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54329 AN: 151970 Hom.: 9858 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.358 AC: 54372 AN: 152088 Hom.: 9872 Cov.: 33 AF XY: 0.353 AC XY: 26247 AN XY: 74340

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.412

Alfa AF: 0.367 Hom.: 4859

Bravo AF: 0.368

Asia WGS AF: 0.354 AC: 1232 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.4
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1459019; hg19: chr10-14712443;