chr2-96957273-G-A

Variant names:

• chr2-96957273-G-A
• rs1796045
• NM_001122646.3:c.887+3015C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ENSG00000293951 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001122646.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM178B	NM_001122646.3	MANE Select	c.887+3015C>T		intron	N/A	NP_001116118.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM178B	ENST00000490605.3	TSL:5 MANE Select	c.887+3015C>T		intron	N/A	ENSP00000429896.1
	ENSG00000293951	ENST00000720068.1		n.126-14G>A		intron	N/A

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

African (AFR) AF: 0.807 AC: 33480 AN: 41496

American (AMR) AF: 0.641 AC: 9794 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.797 AC: 2768 AN: 3472

East Asian (EAS) AF: 0.455 AC: 2350 AN: 5168

South Asian (SAS) AF: 0.356 AC: 1717 AN: 4818

European-Finnish (FIN) AF: 0.722 AC: 7634 AN: 10576

Middle Eastern (MID) AF: 0.829 AC: 242 AN: 292

European-Non Finnish (NFE) AF: 0.798 AC: 54272 AN: 67994

Other (OTH) AF: 0.763 AC: 1611 AN: 2112

Alfa AF: 0.762 Hom.: 22428

Bravo AF: 0.756

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	13
DANN	Benign	0.78
PhyloP100		0.51
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs1796045; hg19: chr2-97623010;