rs2116519

chr1-166160981-G-A

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM78B	NM_001017961.5	c.263+5005C>T		intron_variant		ENST00000354422.4
FAM78B	NM_001320302.2	c.263+5005C>T		intron_variant
FAM78B	NR_135199.2	n.1016+5005C>T		intron_variant, non_coding_transcript_variant
FAM78B	NR_163271.1	n.770+5005C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM78B	ENST00000354422.4	c.263+5005C>T		intron_variant		2	NM_001017961.5	P1
	ENST00000451784.1	n.306+3809C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.521

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.745

Gnomad4 OTH AF: 0.612

Alfa AF: 0.719 Hom.: 78175

Bravo AF: 0.601

Asia WGS AF: 0.517 AC: 1799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	3.3
Dann	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs2116519; hg19: chr1-166130218;