rs10874468

Positions:

• chr2-96930254-G-A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM178B	NM_001122646.3	c.1079-934C>T		intron_variant		ENST00000490605.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM178B	ENST00000490605.3	c.1079-934C>T		intron_variant		5	NM_001122646.3	P1
FAM178B	ENST00000478671.6	n.210-934C>T		intron_variant, non_coding_transcript_variant		4
FAM178B	ENST00000520074.1	n.445-934C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.246

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.680

Gnomad4 OTH AF: 0.550

Alfa AF: 0.639 Hom.: 63259

Bravo AF: 0.482

Asia WGS AF: 0.346 AC: 1204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.9
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10874468; hg19: chr2-97595991;