6-3850959-C-T

Variant names:

• chr6-3850959-C-T
• rs6597007
• NM_012135.3:c.*170C>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012135.3(FAM50B):​c.*170C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000101 in 987,600 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0000010 (0 hom.)
• Consequence: FAM50B NM_012135.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.21
• Publications: 15 publications found

Genes affected

FAM50B (HGNC:18789): (family with sequence similarity 50 member B) This gene contains an intronless ORF that arose from ancestral retroposition. The encoded protein is related to a plant protein that plays a role in the circadian clock. This gene is adjacent to a differentially methylated region (DMR) and is imprinted and paternally expressed in many tissues. [provided by RefSeq, Nov 2015]

ENSG00000301665 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012135.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM50B	NM_012135.3	MANE Select	c.*170C>T		3_prime_UTR	Exon 2 of 2	NP_036267.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FAM50B	ENST00000648326.1	MANE Select	c.*170C>T		3_prime_UTR	Exon 2 of 2	ENSP00000496837.1
	ENSG00000301665	ENST00000780705.1		n.538G>A		non_coding_transcript_exon	Exon 3 of 5
	FAM50B	ENST00000380274.2	TSL:6	c.*170C>T		3_prime_UTR	Exon 1 of 1	ENSP00000369627.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000101 AC: 1 AN: 987600 Hom.: 0 Cov.: 13 AF XY: 0.00 AC XY: 0 AN XY: 489064

African (AFR) AF: 0.00 AC: 0 AN: 22242

American (AMR) AF: 0.00 AC: 0 AN: 19342

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 16920

East Asian (EAS) AF: 0.00 AC: 0 AN: 33190

South Asian (SAS) AF: 0.00 AC: 0 AN: 56056

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44040

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3044

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 749626

Other (OTH) AF: 0.0000232 AC: 1 AN: 43140

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 182

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.094
DANN	Benign	0.23
PhyloP100		-4.2

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: rs6597007; hg19: chr6-3851193;