rs2738820

chr6-170292171-C-Achr6-170292171-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001286379.2(FAM120B):c.15+1099C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,106 control chromosomes in the GnomAD database, including 20,539 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 0.50 (20539 hom., cov: 33)
• Consequence: FAM120B NM_001286379.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.783

Genes affected

FAM120B (HGNC:21109): (family with sequence similarity 120 member B) Predicted to be involved in fat cell differentiation and peroxisome proliferator activated receptor signaling pathway. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

DLL1 (HGNC:2908): (delta like canonical Notch ligand 1) DLL1 is a human homolog of the Notch Delta ligand and is a member of the delta/serrate/jagged family. It plays a role in mediating cell fate decisions during hematopoiesis. It may play a role in cell-to-cell communication. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM120B	NM_001286379.2	c.15+1099C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM120B	ENST00000630384.2	c.15+1099C>A		intron_variant		2		A2
DLL1	ENST00000630500.1	c.-346-1686G>T		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75742 AN: 151988 Hom.: 20539 Cov.: 33

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.579

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.00867

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75756 AN: 152106 Hom.: 20539 Cov.: 33 AF XY: 0.493 AC XY: 36659 AN XY: 74362

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.543

Gnomad4 ASJ AF: 0.588

Gnomad4 EAS AF: 0.00907

Gnomad4 SAS AF: 0.443

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.508

Alfa AF: 0.576 Hom.: 9959

Bravo AF: 0.487

Asia WGS AF: 0.222 AC: 775 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
Cadd	Benign	16
Dann	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2738820; hg19: chr6-170601259;