rs1796045

chr2-96957273-G-Achr2-96957273-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001122646.3(FAM178B):c.887+3015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,108 control chromosomes in the GnomAD database, including 44,351 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 0.75 (44351 hom., cov: 32)
• Consequence: FAM178B NM_001122646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.513

Genes affected

FAM178B (HGNC:28036): (family with sequence similarity 178 member B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.8 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM178B	NM_001122646.3	c.887+3015C>T		intron_variant		ENST00000490605.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM178B	ENST00000490605.3	c.887+3015C>T		intron_variant		5	NM_001122646.3	P1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114626 AN: 151988 Hom.: 44338 Cov.: 32

Gnomad AFR AF: 0.807

Gnomad AMI AF: 0.879

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.797

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.356

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.798

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.754 AC: 114668 AN: 152108 Hom.: 44351 Cov.: 32 AF XY: 0.742 AC XY: 55177 AN XY: 74354

Gnomad4 AFR AF: 0.807

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.797

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.356

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.798

Gnomad4 OTH AF: 0.763

Alfa AF: 0.758 Hom.: 19745

Bravo AF: 0.756

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
Cadd	Benign	13
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1796045; hg19: chr2-97623010;