6-170293341-T-C

Position:

• chr6-170293341-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001286379.2(FAM120B):​c.15+2269T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,054 control chromosomes in the GnomAD database, including 1,363 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 0.074 (1363 hom., cov: 32)
• Consequence: FAM120B NM_001286379.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.921

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.561 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FAM120B	NM_001286379.2	c.15+2269T>C		intron_variant			NP_001273308.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM120B	ENST00000630384.2	c.15+2269T>C		intron_variant		2		ENSP00000485745.1
DLL1	ENST00000630500.1	c.-346-2856A>G		intron_variant		4		ENSP00000486351.1

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11243 AN: 151936 Hom.: 1361 Cov.: 32

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0668

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00584

Gnomad OTH AF: 0.0536

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

GnomAD4 genome AF: 0.0741 AC: 11264 AN: 152054 Hom.: 1363 Cov.: 32 AF XY: 0.0825 AC XY: 6128 AN XY: 74318

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0673

Gnomad4 ASJ AF: 0.0109

Gnomad4 EAS AF: 0.578

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.00584

Gnomad4 OTH AF: 0.0573

Alfa AF: 0.0390 Hom.: 47

Bravo AF: 0.0750

Asia WGS AF: 0.351 AC: 1218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	16
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17860704; hg19: chr6-170602429;