rs6471680

Variant names:

• chr8-58089053-G-A
• rs6471680
• NM_001377989.1:c.-325+13430G>A

Variant summary

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

The NM_001377989.1(FAM110B):​c.-325+13430G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 152,128 control chromosomes in the GnomAD database, including 9,936 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 0.31 (9936 hom., cov: 33)
• Consequence: FAM110B NM_001377989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 0 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FAM110B	NM_001377989.1	c.-325+13430G>A		intron_variant	Intron 3 of 3	ENST00000519262.6	NP_001364918.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM110B	ENST00000519262.6	c.-325+13430G>A		intron_variant	Intron 3 of 3	2	NM_001377989.1	ENSP00000509301.1

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46871 AN: 152010 Hom.: 9901 Cov.: 33

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.309 AC: 46964 AN: 152128 Hom.: 9936 Cov.: 33 AF XY: 0.302 AC XY: 22475 AN XY: 74366

African (AFR) AF: 0.604 AC: 25056 AN: 41466

American (AMR) AF: 0.207 AC: 3165 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.297 AC: 1030 AN: 3468

East Asian (EAS) AF: 0.160 AC: 828 AN: 5172

South Asian (SAS) AF: 0.206 AC: 993 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1346 AN: 10598

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13602 AN: 67984

Other (OTH) AF: 0.296 AC: 626 AN: 2114

Alfa AF: 0.233 Hom.: 19500

Bravo AF: 0.328

Asia WGS AF: 0.222 AC: 774 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.8
DANN	Benign	0.63
PhyloP100		-0.015
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: rs6471680; hg19: chr8-59001612;