rs67631072

Variant names:

• chr1-37996149-C-T
• rs67631072
• ENST00000882675.1:c.*1256G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000882675.1(FHL3):​c.*1256G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 152,098 control chromosomes in the GnomAD database, including 15,649 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 0.42 (15649 hom., cov: 34)
• Consequence: FHL3 ENST00000882675.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87
• Publications: 31 publications found

Genes affected

FHL3 (HGNC:3704): (four and a half LIM domains 3) The protein encoded by this gene is a member of a family of proteins containing a four-and-a-half LIM domain, which is a highly conserved double zinc finger motif. The encoded protein has been shown to interact with the cancer developmental regulators SMAD2, SMAD3, and SMAD4, the skeletal muscle myogenesis protein MyoD, and the high-affinity IgE beta chain regulator MZF-1. This protein may be involved in tumor suppression, repression of MyoD expression, and repression of IgE receptor expression. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000882675.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FHL3	ENST00000882675.1		c.*1256G>A		3_prime_UTR	Exon 5 of 5	ENSP00000552734.1

Frequencies

GnomAD3 genomes AF: 0.421 AC: 63957 AN: 151984 Hom.: 15653 Cov.: 34

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.579

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.420 AC: 63951 AN: 152098 Hom.: 15649 Cov.: 34 AF XY: 0.422 AC XY: 31397 AN XY: 74354

African (AFR) AF: 0.163 AC: 6780 AN: 41552

American (AMR) AF: 0.431 AC: 6582 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.492 AC: 1698 AN: 3450

East Asian (EAS) AF: 0.344 AC: 1776 AN: 5168

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4820

European-Finnish (FIN) AF: 0.579 AC: 6139 AN: 10596

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37517 AN: 67908

Other (OTH) AF: 0.435 AC: 918 AN: 2110

Alfa AF: 0.490 Hom.: 2485

Bravo AF: 0.393

Asia WGS AF: 0.404 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	20
DANN	Benign	0.85
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs67631072; hg19: chr1-38461821;