rs6597007

chr6-3850959-C-Gchr6-3850959-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FAM50B	NM_012135.3	c.*170C>G		3_prime_UTR_variant	2/2	ENST00000648326.1
FAM50B	XM_017010729.2	c.*170C>G		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FAM50B	ENST00000648326.1	c.*170C>G		3_prime_UTR_variant	2/2		NM_012135.3	P1
	ENST00000454396.2	n.80-4511C>G		intron_variant, non_coding_transcript_variant		5
	ENST00000648025.1	n.76+18948C>G		intron_variant, non_coding_transcript_variant
FAM50B	ENST00000380274.2	c.*170C>G		3_prime_UTR_variant	1/1			P1

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

Gnomad4 AFR exome AF: 0.264

Gnomad4 AMR exome AF: 0.0840

Gnomad4 ASJ exome AF: 0.109

Gnomad4 EAS exome AF: 0.202

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.102

Gnomad4 NFE exome AF: 0.117

Gnomad4 OTH exome AF: 0.133

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

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0990

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.100

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.143

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.085
Dann	Benign	0.43

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

Publications

LitVar

Other links and lift over

dbSNP: rs6597007; hg19: chr6-3851193;