chr10-14618200-C-T

Position:

• chr10-14618200-C-T

Variant summary

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

The NM_031453.4(FAM107B):​c.469+49434G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,030 control chromosomes in the GnomAD database, including 4,637 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 0.24 (4637 hom., cov: 31)
• Consequence: FAM107B NM_031453.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM107B	NM_031453.4	c.469+49434G>A		intron_variant		ENST00000181796.7	NP_113641.2
FAM107B	NM_001282695.2	c.-123+49434G>A		intron_variant			NP_001269624.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM107B	ENST00000181796.7	c.469+49434G>A		intron_variant		2	NM_031453.4	ENSP00000181796
FAM107B	ENST00000487335.5	c.469+49434G>A		intron_variant, NMD_transcript_variant		1		ENSP00000420273

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36755 AN: 151912 Hom.: 4629 Cov.: 31

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.242 AC: 36809 AN: 152030 Hom.: 4637 Cov.: 31 AF XY: 0.240 AC XY: 17825 AN XY: 74322

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.234

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.248

Gnomad4 OTH AF: 0.214

Alfa AF: 0.242 Hom.: 6923

Bravo AF: 0.251

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7921651; hg19: chr10-14660199;