rs1334891

Variant names:

• chr10-97321114-G-T
• rs1334891
• NM_005479.4:c.*821G>T

Variant summary

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

The NM_005479.4(FRAT1):​c.*821G>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 0.247 in 167,120 control chromosomes in the GnomAD database, including 6,053 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 0.25 (5612 hom., cov: 32)
  • Exomes 𝑓: 0.25 (441 hom.)
• Consequence: FRAT1 NM_005479.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 13 publications found

Genes affected

FRAT1 (HGNC:3944): (FRAT regulator of WNT signaling pathway 1) The protein encoded by this gene belongs to the GSK-3-binding protein family. The protein inhibits GSK-3-mediated phosphorylation of beta-catenin and positively regulates the Wnt signaling pathway. It may function in tumor progression and in lymphomagenesis. [provided by RefSeq, Oct 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FRAT1	NM_005479.4	c.*821G>T		3_prime_UTR_variant	Exon 1 of 1	ENST00000371021.5	NP_005470.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FRAT1	ENST00000371021.5	c.*821G>T		3_prime_UTR_variant	Exon 1 of 1	6	NM_005479.4	ENSP00000360060.3
FRAT1	ENST00000490980.1	n.374G>T		non_coding_transcript_exon_variant	Exon 1 of 2	2

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37590 AN: 152054 Hom.: 5621 Cov.: 32

Gnomad AFR AF: 0.0700

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.242

Gnomad FIN AF: 0.247

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.294

GnomAD4 exome AF: 0.246 AC: 3672 AN: 14948 Hom.: 441 Cov.: 0 AF XY: 0.245 AC XY: 1744 AN XY: 7118

African (AFR) AF: 0.167 AC: 1 AN: 6

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.245 AC: 3594 AN: 14690

Middle Eastern (MID) AF: 0.500 AC: 1 AN: 2

European-Non Finnish (NFE) AF: 0.279 AC: 39 AN: 140

Other (OTH) AF: 0.350 AC: 35 AN: 100

GnomAD4 genome AF: 0.247 AC: 37579 AN: 152172 Hom.: 5612 Cov.: 32 AF XY: 0.246 AC XY: 18270 AN XY: 74400

African (AFR) AF: 0.0698 AC: 2901 AN: 41548

American (AMR) AF: 0.311 AC: 4749 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1975 AN: 5166

South Asian (SAS) AF: 0.243 AC: 1174 AN: 4828

European-Finnish (FIN) AF: 0.247 AC: 2622 AN: 10600

Middle Eastern (MID) AF: 0.296 AC: 87 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22012 AN: 67972

Other (OTH) AF: 0.294 AC: 619 AN: 2108

Alfa AF: 0.300 Hom.: 11679

Bravo AF: 0.248

Asia WGS AF: 0.284 AC: 987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.6
DANN	Benign	0.78
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism (auto)

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: rs1334891; hg19: chr10-99080871; COSMIC: COSV64017486;