rs285753

Positions:

• chr15-92674847-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM174B	ENST00000557398.2	c.-90+24193C>T		intron_variant		4

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;