NM_012135.3:c.*170C>G

Variant names:

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

Variant summary

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

The NM_012135.3(FAM50B):​c.*170C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 1,138,892 control chromosomes in the GnomAD database, including 9,999 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 0.15 (2137 hom., cov: 33)
  • Exomes 𝑓: 0.12 (7862 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

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>G		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>G		3_prime_UTR	Exon 2 of 2	ENSP00000496837.1
	ENSG00000301665	ENST00000780705.1		n.538G>C		non_coding_transcript_exon	Exon 3 of 5
	FAM50B	ENST00000380274.2	TSL:6	c.*170C>G		3_prime_UTR	Exon 1 of 1	ENSP00000369627.1

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23456 AN: 152062 Hom.: 2134 Cov.: 33

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0992

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.100

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.145

GnomAD4 exome AF: 0.122 AC: 120250 AN: 986712 Hom.: 7862 Cov.: 13 AF XY: 0.121 AC XY: 59123 AN XY: 488632

African (AFR) AF: 0.264 AC: 5862 AN: 22212

American (AMR) AF: 0.0840 AC: 1625 AN: 19340

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 1847 AN: 16914

East Asian (EAS) AF: 0.202 AC: 6689 AN: 33178

South Asian (SAS) AF: 0.106 AC: 5922 AN: 56038

European-Finnish (FIN) AF: 0.102 AC: 4478 AN: 44036

Middle Eastern (MID) AF: 0.141 AC: 428 AN: 3040

European-Non Finnish (NFE) AF: 0.117 AC: 87673 AN: 748860

Other (OTH) AF: 0.133 AC: 5726 AN: 43094

GnomAD4 genome AF: 0.154 AC: 23472 AN: 152180 Hom.: 2137 Cov.: 33 AF XY: 0.152 AC XY: 11325 AN XY: 74396

African (AFR) AF: 0.251 AC: 10422 AN: 41470

American (AMR) AF: 0.0990 AC: 1514 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 408 AN: 3472

East Asian (EAS) AF: 0.221 AC: 1144 AN: 5174

South Asian (SAS) AF: 0.100 AC: 484 AN: 4818

European-Finnish (FIN) AF: 0.106 AC: 1119 AN: 10604

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7991 AN: 68024

Other (OTH) AF: 0.143 AC: 303 AN: 2116

Alfa AF: 0.120 Hom.: 182

Bravo AF: 0.160

Asia WGS AF: 0.137 AC: 479 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.085
DANN	Benign	0.43
PhyloP100		-4.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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;