rs10874468

Variant names:

• chr2-96930254-G-A
• rs10874468
• NM_001122646.3:c.1079-934C>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.1079-934C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.522 in 138,860 control chromosomes in the GnomAD database, including 21,425 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 (21425 hom., cov: 24)
• Consequence: FAM178B NM_001122646.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM178B	NM_001122646.3	MANE Select	c.1079-934C>T		intron	N/A	NP_001116118.2	Q8IXR5-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM178B	ENST00000490605.3	TSL:5 MANE Select	c.1079-934C>T		intron	N/A	ENSP00000429896.1	Q8IXR5-3
	FAM178B	ENST00000478671.6	TSL:4	n.210-934C>T		intron	N/A
	FAM178B	ENST00000520074.1	TSL:5	n.445-934C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.522 AC: 72491 AN: 138824 Hom.: 21424 Cov.: 24

Gnomad AFR AF: 0.246

Gnomad AMI AF: 0.665

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.613

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.522 AC: 72493 AN: 138860 Hom.: 21425 Cov.: 24 AF XY: 0.513 AC XY: 34137 AN XY: 66496

African (AFR) AF: 0.246 AC: 8656 AN: 35186

American (AMR) AF: 0.486 AC: 6368 AN: 13090

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1877 AN: 3430

East Asian (EAS) AF: 0.337 AC: 1608 AN: 4776

South Asian (SAS) AF: 0.311 AC: 1370 AN: 4400

European-Finnish (FIN) AF: 0.663 AC: 5186 AN: 7822

Middle Eastern (MID) AF: 0.609 AC: 167 AN: 274

European-Non Finnish (NFE) AF: 0.680 AC: 45593 AN: 67034

Other (OTH) AF: 0.550 AC: 1076 AN: 1958

Alfa AF: 0.611 Hom.: 94165

Bravo AF: 0.482

Asia WGS AF: 0.346 AC: 1204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.43
PhyloP100		-0.027
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: rs10874468; hg19: chr2-97595991;