chr8-58072215-A-G

Variant names:

• chr8-58072215-A-G
• rs10504244
• NM_001377989.1:c.-413-3320A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
FAM110B	NM_001377989.1	c.-413-3320A>G		intron_variant	Intron 2 of 3	ENST00000519262.6	NP_001364918.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM110B	ENST00000519262.6	c.-413-3320A>G		intron_variant	Intron 2 of 3	2	NM_001377989.1	ENSP00000509301.1

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

African (AFR) AF: 0.0868 AC: 3609 AN: 41556

American (AMR) AF: 0.275 AC: 4203 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1276 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1475 AN: 5164

South Asian (SAS) AF: 0.320 AC: 1542 AN: 4816

European-Finnish (FIN) AF: 0.448 AC: 4723 AN: 10552

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27586 AN: 67976

Other (OTH) AF: 0.275 AC: 582 AN: 2114

Alfa AF: 0.361 Hom.: 7927

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
PhyloP100		-0.13
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: rs10504244; hg19: chr8-58984774;