rs2132616

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FAM174B	ENST00000557398.2	c.-90+3890G>C		intron_variant	Intron 2 of 3	4		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

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;