rs10504244

chr8-58072215-A-G

Variant summary

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

The NM_001377989.1(FAM110B):c.-413-3320A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 152,118 control chromosomes in the GnomAD database, including 8,245 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 0.30 (8245 hom., cov: 32)
• Consequence: FAM110B NM_001377989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.125

Genes affected

FAM110B (HGNC:28587): (family with sequence similarity 110 member B) Located in cytosol and mitochondrion. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM110B	NM_001377989.1	c.-413-3320A>G		intron_variant		ENST00000519262.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM110B	ENST00000519262.6	c.-413-3320A>G		intron_variant		2	NM_001377989.1	P1

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45466 AN: 151998 Hom.: 8246 Cov.: 32

Gnomad AFR AF: 0.0870

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.276

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.299 AC: 45454 AN: 152118 Hom.: 8245 Cov.: 32 AF XY: 0.301 AC XY: 22364 AN XY: 74342

Gnomad4 AFR AF: 0.0868

Gnomad4 AMR AF: 0.275

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.286

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.448

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.275

Alfa AF: 0.367 Hom.: 5813

Bravo AF: 0.276

Asia WGS AF: 0.279 AC: 965 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.2
Dann	Benign	0.81

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504244; hg19: chr8-58984774;