rs2132616

Positions:

• chr15-92695150-C-G
• chr15-92695150-C-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.638 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+3890G>C		intron_variant		4

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

Gnomad4 AFR AF: 0.255

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.463

Gnomad4 EAS AF: 0.657

Gnomad4 SAS AF: 0.493

Gnomad4 FIN AF: 0.726

Gnomad4 NFE AF: 0.633

Gnomad4 OTH AF: 0.514

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2132616; hg19: chr15-93238380;