ENST00000557398.2:c.-90+3890G>C

Variant names:

• chr15-92695150-C-G
• rs2132616
• ENST00000557398.2:c.-90+3890G>C

Variant summary

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

The ENST00000557398.2(FAM174B):​c.-90+3890G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 152,030 control chromosomes in the GnomAD database, including 22,863 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 0.52 (22863 hom., cov: 32)
• Consequence: FAM174B ENST00000557398.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 0 publications found

Genes affected

FAM174B (HGNC:34339): (family with sequence similarity 174 member B) Involved in Golgi organization. Located in Golgi apparatus and plasma membrane. [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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000557398.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM174B	ENST00000557398.2	TSL:4	c.-90+3890G>C		intron	N/A	ENSP00000456099.2

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79071 AN: 151910 Hom.: 22867 Cov.: 32

Gnomad AFR AF: 0.255

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.633

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.520 AC: 79083 AN: 152030 Hom.: 22863 Cov.: 32 AF XY: 0.526 AC XY: 39078 AN XY: 74316

African (AFR) AF: 0.255 AC: 10551 AN: 41442

American (AMR) AF: 0.566 AC: 8648 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1604 AN: 3468

East Asian (EAS) AF: 0.657 AC: 3400 AN: 5176

South Asian (SAS) AF: 0.493 AC: 2375 AN: 4818

European-Finnish (FIN) AF: 0.726 AC: 7663 AN: 10554

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.633 AC: 43019 AN: 67986

Other (OTH) AF: 0.514 AC: 1083 AN: 2108

Alfa AF: 0.569 Hom.: 3141

Bravo AF: 0.495

Asia WGS AF: 0.489 AC: 1701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.1
DANN	Benign	0.72
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs2132616; hg19: chr15-93238380;