rs285753

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM174B	ENST00000557398.2	c.-90+24193C>T		intron_variant	Intron 2 of 3	4		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

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.0371

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.229

Alfa AF: 0.210 Hom.: 2995

Bravo AF: 0.261

Asia WGS AF: 0.178 AC: 620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs285753; hg19: chr15-93218077;