rs2116519

Variant names:

• chr1-166160981-G-A
• rs2116519
• NM_001017961.5:c.263+5005C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001017961.5(FAM78B):​c.263+5005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.615 in 152,074 control chromosomes in the GnomAD database, including 30,494 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 0.61 (30494 hom., cov: 32)
• Consequence: FAM78B NM_001017961.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.637
• Publications: 5 publications found

Genes affected

FAM78B (HGNC:13495): (family with sequence similarity 78 member B)

ENSG00000230898 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001017961.5. 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
	FAM78B	NM_001017961.5	MANE Select	c.263+5005C>T		intron	N/A	NP_001017961.1
	FAM78B	NM_001320302.2		c.263+5005C>T		intron	N/A	NP_001307231.1
	FAM78B	NR_135199.2		n.1016+5005C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM78B	ENST00000354422.4	TSL:2 MANE Select	c.263+5005C>T		intron	N/A	ENSP00000346404.3
	FAM78B	ENST00000338353.4	TSL:1	c.263+5005C>T		intron	N/A	ENSP00000339681.3
	FAM78B	ENST00000435676.2	TSL:2	n.239+5005C>T		intron	N/A	ENSP00000412766.1

Frequencies

GnomAD3 genomes AF: 0.615 AC: 93425 AN: 151956 Hom.: 30488 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.615 AC: 93459 AN: 152074 Hom.: 30494 Cov.: 32 AF XY: 0.611 AC XY: 45445 AN XY: 74320

African (AFR) AF: 0.391 AC: 16210 AN: 41470

American (AMR) AF: 0.607 AC: 9273 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2290 AN: 3472

East Asian (EAS) AF: 0.521 AC: 2683 AN: 5150

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4824

European-Finnish (FIN) AF: 0.722 AC: 7628 AN: 10572

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50657 AN: 67986

Other (OTH) AF: 0.612 AC: 1295 AN: 2116

Alfa AF: 0.698 Hom.: 118467

Bravo AF: 0.601

Asia WGS AF: 0.517 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.69
PhyloP100		0.64
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2116519; hg19: chr1-166130218;