rs285753

Variant names:

• chr15-92674847-G-A
• rs285753
• ENST00000557398.2:c.-90+24193C>T

Variant summary

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

The ENST00000557398.2(FAM174B):​c.-90+24193C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,080 control chromosomes in the GnomAD database, including 6,003 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 0.25 (6003 hom., cov: 32)
• Consequence: FAM174B ENST00000557398.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.280
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.441 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM174B	ENST00000557398.2	TSL:4	c.-90+24193C>T		intron	N/A	ENSP00000456099.2

Frequencies

GnomAD3 genomes AF: 0.254 AC: 38567 AN: 151962 Hom.: 5981 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.0372

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.254 AC: 38612 AN: 152080 Hom.: 6003 Cov.: 32 AF XY: 0.249 AC XY: 18499 AN XY: 74328

African (AFR) AF: 0.446 AC: 18492 AN: 41418

American (AMR) AF: 0.171 AC: 2610 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 635 AN: 3470

East Asian (EAS) AF: 0.0371 AC: 192 AN: 5182

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4816

European-Finnish (FIN) AF: 0.133 AC: 1410 AN: 10582

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13382 AN: 68008

Other (OTH) AF: 0.229 AC: 484 AN: 2114

Alfa AF: 0.211 Hom.: 3498

Bravo AF: 0.261

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.75
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs285753; hg19: chr15-93218077;